Short communication| Volume 33, P106-109, March 2018

Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel

Published:December 05, 2017DOI:


      • 165 AIMs were typed in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel.
      • One locus had statistically significantly different genotype frequencies in the two samples, after Bonferroni correction.
      • The population likelihoods for mainland Japanese and Okinawa Japanese were not significantly different from each other.
      • STRUCTURE and PCA showed that the panel could not differentiate mainland Japanese, Okinawa Japanese, and East Asians.


      We typed 165 AIMs in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel (Thermo Fisher Scientific). None of the 165 SNPs showed significant deviation from Hardy-Weinberg equilibrium in the mainland Japanese. One SNP (rs3943253) showed significant deviation from Hardy-Weinberg equilibrium in Okinawa Japanese. Fisher’s exact tests showed that the genotype frequencies of 14 loci were significantly different (p < 0.05) between the two populations before correction for multiple testing. After Bonferroni correction, only rs671 remained statistically significant (p < 0.0003). This SNP is located in the ALDH2 gene. The mutant A allele is associated with increased side effects after alcohol intake. The frequency of the GG genotype (wild type) was higher in the Okinawa Japanese (78.7%) than in mainland Japanese (34.7%; Bonferroni corrected P < 0.001). For 31 (63.3%) of the mainland Japanese and 42 (89.4%) of Okinawa Japanese, the highest population likelihood was obtained with the Japanese reference population. However, only in a few individuals, the likelihoods were significantly different from those calculated using reference data from neighboring populations. The likelihoods for mainland Japanese and Okinawa Japanese were not significantly different from each other for any of the investigated individuals. STRUCTURE and PCA analyses showed that mainland Japanese, Okinawa Japanese, and East Asians could not be differentiated with the Precision ID Ancestry Panel.


      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'


      Subscribe to Forensic Science International: Genetics
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect


        • Hanihara K.
        Dual structure model for population history of the Japanese.
        Jpn. Rev. 1991; 2: 1-33
        • Jinam T.
        • Kanzawa-Kiriyama H.
        • Saitou N.
        Human genetic diversity in the Japanese Archipelago: dual structure and beyond.
        Genes Genet. Syst. 2015; 90: 147-152
        • Nonaka I.
        • Minaguchi K.
        • Takezaki N.
        Y-chromosomal binary haplogroups in the Japanese population and their relationship to 16 Y-STR polymorphisms.
        Ann. Hum. Genet. 2007; 71: 480-495
        • Hammer M.F.
        • Karafet T.M.
        • Park H.
        • Omoto K.
        • Harihara S.
        • Stoneking M.
        • Horai S.
        Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes.
        J. Hum. Genet. 2006; 51: 47-58
        • Horai S.
        • Murayama K.
        • Hayasaka K.
        • Matsubayashi S.
        • Hattori Y.
        • Fucharoen G.
        • Harihara S.
        • Park K.S.
        • Omoto K.
        • Pan I.H.
        mtDNA polymorphism in East Asian populations, with special reference to the peopling of Japan.
        Am. J. Hum. Genet. 1996; 59: 579-590
        • Tanaka M.
        • Cabrera V.M.
        • González A.M.
        • Larruga J.M.
        • Takeyasu T.
        • Fuku N.
        • Guo L.J.
        • Hirose R.
        • Fujita Y.
        • Kurata M.
        • Shinoda K.
        • Umetsu K.
        • Yamada Y.
        • Oshida Y.
        • Sato Y.
        • Hattori N.
        • Mizuno Y.
        • Arai Y.
        • Hirose N.
        • Ohta S.
        • Ogawa O.
        • Tanaka Y.
        • Kawamori R.
        • Shamoto-Nagai M.
        • Maruyama W.
        • Shimokata H.
        • Suzuki R.
        • Shimodaira H.
        Mitochondrial genome variation in eastern asia and the peopling of Japan.
        Genome Res. 2004; 14: 1832-1850
        • Umetsu K.
        • Tanaka M.
        • Yuasa I.
        • Adachi N.
        • Miyoshi A.
        • Kashimura S.
        • Park K.S.
        • Wei Y.H.
        • Watanabe G.
        • Osawa M.
        Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations.
        Electrophoresis. 2005; 26: 91-98
        • Yamaguchi-Kabata Y.
        • Nakazono K.
        • Takahashi A.
        • Saito S.
        • Hosono N.
        • Kubo M.
        • Nakamura Y.
        • Kamatani N.
        Japanese population structure, based on SNP genotypes from 7003 individuals compared to other ethnic groups: effects on population-based association studies.
        Am. J. Hum. Genet. 2008; 83: 445-456
        • Japanese Archipelago Human Population Genetics Consortium
        • Nishida M.
        • Hirai S.
        • Kawamura H.
        • Oota K.
        • Umetsu R.
        • Kimura J.
        • Ohashi A.
        • Tajima T.
        • Yamamoto H.
        • Tanabe S.
        • Mano Y.
        • Suto T.
        • Kaname K.
        • Naritomi K.
        • Yanagi N.
        • Niikawa K.
        • Omoto K.
        • Tokunaga N.
        The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations.
        J. Hum. Genet. 2012; 57: 787-795
        • Phillips C.
        • Prieto L.
        • Fondevila M.
        • Salas A.
        • Gómez-Tato A.
        • Álvarez-Dios J.
        • Alonso A.
        • Blanco-Verea A.
        • Brión M.
        • Montesino M.
        • Á Carracedo
        • Lareu M.V.
        Ancestry analysis in the 11-M Madrid bomb attack investigation.
        PLoS One. 2009; 4: e6583
        • Børsting C.
        • Morling N.
        Next generation sequencing and its applications in forensic genetics.
        Forensic Sci. Int. Genet. 2015; 18: 78-89
        • Yang Y.
        • Xie B.
        • Yan J.
        Application of next-generation sequencing technology in forensic science.
        Genomics Proteomics Bioinf. 2014; 12: 190-197
        • Themudo G.E.
        • Mogensen H.S.
        • Børsting C.
        • Morling N.
        Frequencies of HID-ion ampliseq ancestry panel markers among Greenlanders.
        Forensic Sci. Int. Genet. 2016; 24: 60-64
        • Hollard C.
        • Keyser C.
        • Delabarde T.
        • Gonzalez1 A.
        • Lamego C.V.
        Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case.
        Int. J. Legal Med. 2017; 131: 351-358
        • Kidd K.K.
        • Speed W.C.
        • Pakstis A.J.
        • Furtado M.R.
        • Fang R.
        • Madbouly A.
        • Maiers M.
        • Middha M.
        • Friedlaender F.R.
        • Kidd J.R.
        Progress toward an efficient panel of SNPs for ancestry inference.
        Forensic Sci. Int. Genet. 2014; 10: 23-32
        • Kosoy R.
        • Nassir R.
        • Tian C.
        • White P.A.
        • Butler L.M.
        • Silva G.
        • Seldin M.F.
        Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.
        Hum. Mutat. 2009; 30: 69-78
        • Pereira V.
        • Mogensen H.S.
        • Børsting C.
        • Morling N.
        Evaluation of the Precision ID Ancestry Panel for crime case work: a SNP typing assay developed for typing of 165 ancestral informative markers.
        Forensic Sci Int. Genet. 2017; 28: 138-145
        • Excoffier L.
        • Lischer H.E.L.
        Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.
        Mol. Ecol. Resour. 2010; 10: 564-567
        • Rousset F.
        Genepop ‘007: a complete reimplementation of the genepop sotware for Windows and Linux.
        Mol. Ecol. Resour. 2008; 8: 103-106
        • Bonferroni C.E.
        Teoria Statistica Delle Classi E Calcolo Delle Probabilità, Pubblicazioni Del Regio Istituto Superiore Di Scienze Economiche E Commerciali Di Firenze. 8. 1936: 3-62
        • R Core Team
        R: A Language and Environment for Statistical Computing.
        R Foundation for Statistical Computing, Vienna, Austria2013
        • Chakraborty R.
        • Srinivasan M.R.
        • Daiger S.F.
        Evaluation of standard error and confidence intervals of estimated multilocus genotype probabilities and their implications in DNA Forensics.
        Am. J. Hum. Genet. 1993; 52: 60-70
        • Šidák Z.
        Rectangular confidence regions for the means of multivariate normal distributions.
        J. Am. Stat. Assoc. 1967; 62: 626-633
        • Pritchard J.K.
        • Stephens M.
        • Donnelly P.
        Inference of population structure using multilocus genotype data.
        Genet. Soc. Am. 2000; 155: 945-959
        • Falush D.
        • Stephens M.
        • Pritchard J.K.
        Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.
        Genetics. 2003; 164: 1567-1587
        • Earl D.A.
        • vonHoldt B.M.
        STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method.
        Conserv. Genet. Resour. 2011; 4: 359-361
        • Evanno G.
        • Regnaut S.
        • Goudet J.
        Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
        Mol. Ecol. 2005; 14: 2611-2620
        • Jakobsson M.
        • Rosenberg N.A.
        CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure.
        Bioinformatics. 2007; 23: 1801-1806
        • Rosenberg N.A.
        DISTRUCT: a program for the graphical display of population structure.
        Mol. Ecol. Notes. 2004; 4: 137-138
        • Yoshida A.
        • Huang I.Y.
        • Ikawa M.
        Molecular abnormality of an inactive aldehyde dehydrogenase variant commonly found in Orientals.
        Proc. Natl. Acad. Sci. U.S.A. 1984; 81: 258-261
        • Shibuya A.
        • Yoshida A.
        Frequency of the atypical aldehyde dehydrogenase-2 gene (ALDH22) in Japanese and Caucasians.
        Am. J. Hum. Genet. 1988; 43: 741-743
        • Koganebuchi K.
        • Haneji K.
        • Toma T.
        • Joh K.
        • Soejima H.
        • Fujimoto K.
        • Ishida H.
        The allele frequency of ALDH2*Glu504Lys and ADH1B*Arg47His for the Ryukyu islanders and their history of expansion among East Asians.
        Am. J. Hum. Biol. 2017; 29
        • Santos C.
        • Phillips C.
        • Fondevila M.
        • Daniel R.
        • van Oorschot R.A.
        • Burchard E.G.
        • Schanfield M.S.
        • Souto L.
        • Uacyisrael J.
        • Via M.
        • Carracedo A.
        • Lareu M.V.
        Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.
        Forensic Sci. Int. Genet. 2016; 20: 71-80
        • Li C.X.
        • Pakstis A.J.
        • Jiang L.
        • Wei Y.L.
        • Sun Q.F.
        • Wu H.
        • Bulbul O.
        • Wang P.
        • Kang L.L.
        • Kidd J.R.
        • Kidd K.K.
        A panel of 74 AISNPs: improved ancestry inference within eastern asia.
        Forensic Sci. Int. Genet. 2016; 23: 101-110