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JapanesePlex: a method for identification of being Japanese using Japanese-specific SNPs

Research Project

Project/Area Number 23590849
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Legal medicine
Research InstitutionTottori University

Principal Investigator

YUASA Isao  鳥取大学, 医学部, 准教授 (00093633)

Co-Investigator(Renkei-kenkyūsha) UMETSU Kazuo  山形大学, 医学部, 准教授 (10091828)
Research Collaborator AKANE Atsushi  関西医科大学, 医学部, 教授 (70202520)
Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2013: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2012: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2011: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords日本人 / 特異遺伝子 / 個人識別 / PCR / DNA解析 / 集団特異遺伝子 / PCR / DNA解析
Research Abstract

To find out Japanese-specific SNPs, a total of 875 DNA samples from Japanese in Tottori and Okinawa, Koreans, Mongolians, Hans, Tibetans, Germans and Africans were investigated. Sixty-seven (nearly) Japanese-specific SNPs were observed. Of them, 57 showed the highest frequencies in Okinawa, and 43 were also observed in Koreans at lower frequencies. DNA samples from Jomon remains in Hokkaido were investigated for three SNPs at the GALNT11, H19 and PLA2G12A genes, and showed higher frequencies in every SNP than those from Okinawa, suggesting that the SNPs observed at the highest frequencies in Okinawa were of Jomon lineage. For forensic practice, 50 SNPs with high frequency and no linkage disequilibrium were selected. A multiplex typing method based on single-based primer extension technology were established. This JapanesePlex method permitted the identification of being Japanese with high probability.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (33 results)

All 2013 2012 2011 Other

All Journal Article (23 results) (of which Peer Reviewed: 23 results) Presentation (10 results)

  • [Journal Article] De novo mutations in SLC35A2 encoding a UDP-galactose transporter cause early-onset epileptic encephalopathy2013

    • Author(s)
      Kodera H, Nakamura K, Osaka H, Maegaki Y, Haginoya K, Mizumoto S, Kato M, Okamoto N, Iai M, Kondo Y, Nishiyama K, Tsurusaki Y, Nakashima M, Miyake N, Hayasaka K, Sugahara K, Yuasa I, Wada Y, Matsumoto N, Saitsu H
    • Journal Title

      Human Mutation

      Volume: 34(12) Pages: 1708-1714

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Near fixation of 374l allele frequencies of the skin pigmentation gene SLC45A2 in Africa2013

    • Author(s)
      Lucotte G, Yuasa I
    • Journal Title

      Biochemical Genetics

      Volume: 51(9/10) Pages: 655-665

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A hypervariable STR polymorphism in the CFI gene : Southern origin of East-Asian-specific group H alleles2013

    • Author(s)
      Yuasa I, Jin F, Harihara S, Matsusue A, Fujihara J, Takeshita H, Akane A, Umetsu K, Saitou N, Chattopadhyay PK
    • Journal Title

      Legal Medicine

      Volume: 15(5) Pages: 239-243

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A commentary on assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree2013

    • Author(s)
      Yuasa I
    • Journal Title

      Journal of Human Genetics

      Volume: 58(4) Pages: 181-181

    • NAID

      10031169416

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A hypervariable STR polymorphism in the CFI gene : mutation rate and no linkage disequilibrium with FGA2013

    • Author(s)
      Yuasa I, Nakayashiki N, Umetsu K, Nishimukai H, Matsusue A, Dewa K
    • Journal Title

      Legal Medicine

      Volume: 15(3) Pages: 161-163

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] A hypervariable STR polymorphism in the CFI gene: mutation rate and no linkage disequilibrium with FGA.2013

    • Author(s)
      Yuasa I, Nakayashiki N, Umetsu K, Nishimukai H, Matsusue A, Dewa K:
    • Journal Title

      Legal Medicine

      Volume: 15巻3号 Issue: 3 Pages: 161-163

    • DOI

      10.1016/j.legalmed.2012.10.005

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chattopadhyay PK.; A hypervariable STR polymorphism in the CFI gene : southern origin of East Asian-specific group H alleles2013

    • Author(s)
      Yuasa I., Jin F., Harihara S., Matsusue A., Fujihara J., Takeshita H., Akane A., Umetsu K., Saitou N
    • Journal Title

      Leg. Med. (Tokyo)

      Volume: Vol.15 Issue: 5 Pages: 239-243

    • DOI

      10.1016/j.legalmed.2013.04.001

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Near fixation of 374l allele frequencies of the skin pigmentation gene SLC45A2 in Africa.2013

    • Author(s)
      Lucotte G, Yuasa I
    • Journal Title

      Biochemical Genetics

      Volume: 51巻9/10号 Issue: 9-10 Pages: 655-665

    • DOI

      10.1007/s10528-013-9595-8

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] De novo mutations in SLC35A2 encoding a UDP-galactose transporter cause early-onset epileptic encephalopathy2013

    • Author(s)
      Kodera H, Nakamura K, Osaka H, Maegaki Y, Haginoya K, Mizumoto S, Kato M, Okamoto N, Iai M, Kondo Y, Nishiyama K, Tsurusaki Y, Nakashima M, Miyake N, Hayasaka K, Sugahara K, Yuasa I, Wada Y, Matsumoto N, Saitsu H.
    • Journal Title

      Hum Mutat

      Volume: 34 Issue: 12 Pages: 1708-1714

    • DOI

      10.1002/humu.22446

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Replication study of the association of SNPs in the LHX3-QSOX2 and IGF1 loci with adult height in the Japanese population; wide-ranging comparison of each SNP genotype distribution2012

    • Author(s)
      Fujihara J, Takeshita H, Kimura- Kataoka K, Yuasa I, Iida R, Ueki M, Nagao M, Kominato Y, Yasuda T
    • Journal Title

      Legal Medicine

      Volume: 14(4) Pages: 205-208

    • NAID

      120005308245

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Non-synonymous single-nucleotide polymorphisms of the human apoptosis- related endonuclease–DNA fragmenta- tion factor beta polypeptide, endo- nuclease G, and flap endonuclease-1–genes show a low degree of genetic heterogeneity2012

    • Author(s)
      Takeshita H, Fujihara J, Ueki M, Iida R, Koda Y, Soejima M, Yuasa I, Kato H, Nakajima T, Kominato Y, Yasuda T
    • Journal Title

      DNA and Cell Biology

      Volume: 31(1) Pages: 36-42

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Three Japanese patients with beta- ketothiolase deficiency who share a mutation, c.431A>C (H144P) in ACAT1: subtle abnormality in urinary organic acid analysis and blood acylcarnitine analysis using tandem mass spectrome- try2012

    • Author(s)
      Fukao T, Maruyama S, Ohura T, Hasegawa Y, Toyoshima M,. Haapalainen AM, Kuwada N, Imamura M, Yuasa I, Wierenga RK, Yamaguchi S, Kondo N
    • Journal Title

      JIMD Reports

      Volume: 3 Pages: 107-115

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Nonsynonymous single-nucleotide polymorphisms of the human apoptosis-related endonuclease-DNA fragmentation factor beta polypeptide, endonuclease G, and Flap endonuclease 1-genes show a low degree of genetic heterogeneity2012

    • Author(s)
      H.Takeshita
    • Journal Title

      DNA and Cell Biology

      Volume: 31 Issue: 1 Pages: 36-42

    • DOI

      10.1089/dna.2011.1293

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Replication study of the association of SNPs in the LHX3-QSOX2 and IGF1 loci with adult height in the Japanese population ; wide-ranging comparison of each SNP genotype distribution2012

    • Author(s)
      Junko Fujihara
    • Journal Title

      Legal Medicine

      Volume: (in press) Issue: 4 Pages: 275-280

    • DOI

      10.1016/j.legalmed.2012.02.001

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] The distribution of H19HP haplotypes in Asian populations. Forensic Science International2011

    • Author(s)
      Nakayashiki N, Fujita M, Dewa K, Ding M, Wei W, Wang X, Yamamoto T, Yuasa I
    • Journal Title

      Genetics Supplement Series

      Volume: 3(1)

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transferrin mutations at the glycosylation site complicate diagnosis of congenital disorders of glycosylation type I2011

    • Author(s)
      Guillard M, Wada Y, Hansikova H, Yuasa I, Vesela K, Ondruskova N, Kadoya M, Janssen A, Van den Heuvel LP, Morava E, Zeman J, Wevers RA, Lefeber DJ
    • Journal Title

      J Inherit Metab Dis

      Volume: 34(4) Pages: 901-906

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Confirmation that SNPs in the high mobility group-A2 gene (HMGA2) are associated with adult height in the Japanese population; wide-ranging population survey of height-related SNPs in HMGA22011

    • Author(s)
      Takeshita H, Fujihara J. Soejima M, Koda Y, Kimura-Kataoka K, Ono R, MuroT, Tongu M, Yuasa I, Iida, R, Ueki M, Yasuda T
    • Journal Title

      Electrophoresis

      Volume: 32(14) Pages: 1844-1851

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Global genetic analysis of all single nucleotide polymorphisms in exons of the human deoxyribonuclease I-like 3 gene and their effect on its catalytic activity2011

    • Author(s)
      Ueki M, Fujihara J, Takeshita H, Kimura-Kataoka K, Iida R, Yuasa I, Kato H, Yasuda T
    • Journal Title

      Electrophoresis

      Volume: 32(12) Pages: 1465-1472

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Three Japanese patients with beta-ketothiolase deficiency whoshare a mutation, c.431A>C(H144P) in ACAT1 : subtle abnormality in urinary organic acid analysis and blood acylvcarnitine analysis using tandem mass spectrometry2011

    • Author(s)
      Fukao T
    • Journal Title

      JIMD Reports

      Volume: 3 Pages: 108-115

    • DOI

      10.1007/8904_2011_72

    • ISBN
      9783642249358, 9783642249365
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Transferrin mutations at the glycosylation site complicate diagnosis of congenital disorders of glycosylation type I.2011

    • Author(s)
      Guillard M, Wada Y, Hansikova H, Yuasa I, et al.
    • Journal Title

      Journal of Inherited Metabolic Disease

      Volume: 34 Issue: 4 Pages: 901-906

    • DOI

      10.1007/s10545-011-9311-y

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Distribution of OCA2. 481Thr andOCA2. 615Arg, associated with hypopigmentation, in several additional populations2011

    • Author(s)
      Yuasa I, Harihara S, (他7名、2番目)
    • Journal Title

      Leg Med

      Volume: 13 Issue: 4 Pages: 215-217

    • DOI

      10.1016/j.legalmed.2011.04.003

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Global genetic analysis of all single nucleotide polymorphisms in exons of the human deoxyribonuclease I-like 3 gene and their effect on its catalytic activity2011

    • Author(s)
      Ueki M, Fuiihara J, Takeshita H, Kimura-Kataoka K, Iida R, Yuasa I, Kato H, Yasuda T
    • Journal Title

      Electrophoresis

      Volume: 32 Issue: 12 Pages: 1465-1472

    • DOI

      10.1002/elps.201100064

    • Related Report
      2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Mutations in COG2 Encoding a Subunit of the Conserved Oligomeric Golgi Complex Cause a Congenital Disorder of Glycosylation

    • Author(s)
      Kodera H, Ando N, Yuasa I, Wada Y, Tsurusaki Y, Nakashima M, Miyake N, Saitoh S, Matsumoto N, Saitsu H
    • Journal Title

      Clinical Genetics

      Volume: (印刷中)

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Presentation] 日本人集団並びにドイツ人におけるSCN5A遺伝子R1193Q変異の頻度調査2013

    • Author(s)
      松末綾, 湯浅勲, 梅津和夫, 柏木正之, 原健二, Brian Waters, 高山みお, 高本睦夫, 久保真一
    • Organizer
      第63回日本法医学会学術九州地方集会
    • Place of Presentation
      福岡
    • Related Report
      2013 Final Research Report
  • [Presentation] 日本人およびほぼ日本人特異的SNPについて2013

    • Author(s)
      湯浅勲, 松末綾, 赤根敦, 藤原純子, 竹下治男, 梅津和夫
    • Organizer
      第97次日本法医学会学術全国集会
    • Place of Presentation
      札幌
    • Related Report
      2013 Final Research Report
  • [Presentation] 日本人およびほぼ日本人特異的SNPについて2013

    • Author(s)
      湯浅 勲、松末 綾、赤根 敦、藤原純子、竹下治男、梅津和夫
    • Organizer
      第97次日本法医学会学術全国集会
    • Place of Presentation
      ロイトン札幌(札幌)
    • Related Report
      2013 Annual Research Report
  • [Presentation] ATP6V0A2を原因遺伝子とする先天性グリコシル化異常症にみられた新しい変異2013

    • Author(s)
      湯浅 勲、遠藤 実、石川隆紀、津田祐子、舟塚 真、谷 諭美、西川愛子、伊藤 進、大澤 真木子
    • Organizer
      第22回日本DNA多型学会学術集会
    • Place of Presentation
      仙台市戦災復興記念館(仙台)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 常染色体にみられる日本人特異的遺伝子の分布2012

    • Author(s)
      湯浅勲, 梅津和夫
    • Organizer
      第66回日本人類学会大会
    • Place of Presentation
      日吉
    • Related Report
      2013 Final Research Report
  • [Presentation] PLA2G12Aにみられるほぼ日本人特異的(極東)特異的SNPについて2012

    • Author(s)
      湯浅勲, 入澤淑人, 松末綾, 竹下治男, 針原伸二, 梅津和夫
    • Organizer
      第96次日本法医学会学術全国集会
    • Place of Presentation
      浜松
    • Related Report
      2013 Final Research Report
  • [Presentation] PLA2G12Aにみられるほぼ日本人特異的(極東)特異的SNPについて2012

    • Author(s)
      湯浅 勲、入澤淑人、松末 綾、竹下治男、針原伸二、梅津和夫
    • Organizer
      第96次日本法医学会学術全国集会
    • Place of Presentation
      浜松 アクトシティ浜松
    • Related Report
      2012 Research-status Report
  • [Presentation] 常染色体にみられる日本人特異的遺伝子の分布2012

    • Author(s)
      湯浅 勲、梅津和夫
    • Organizer
      第66回日本人類学会大会
    • Place of Presentation
      慶應義塾大学日吉キャンパス
    • Related Report
      2012 Research-status Report
  • [Presentation] 補体I因子のイントロン7にみられるSTRについて(3)東アジアにおける分布2011

    • Author(s)
      湯浅勲, 遠藤実, 入澤淑人, 針原伸二, 西向弘明, 松末綾, 藤原純子, 竹下治男, 梅津和夫
    • Organizer
      95次日本法医学会学術全国集会
    • Place of Presentation
      福島
    • Related Report
      2013 Final Research Report
  • [Presentation] 補体I因子のイントロン7にみられるSTRについて (3) 東アジアにおける分布2011

    • Author(s)
      湯浅 勲、遠藤実、入澤淑人、他
    • Organizer
      第95次日本法医学会学術全国集会
    • Place of Presentation
      福島 コラッセ福島
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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