Research Article| Volume 60, 102739, September 2022

EASplex: A panel of 308 AISNPs for East Asian ancestry inference using next generation sequencing


      • We developed a multiplex system of 308 AISNPs for East Asian ancestry inference using the NGS technology.
      • The new panel could be used for continental and East Asian ancestry inference.
      • Han Chinese, Korean minorities, and Japanese have different ancestry information.
      • The panel could be used for forensic investigations, population genetics, and clinic applications.


      Ancestry inference is useful in many scientific fields, such as forensic genetics, medical genetics, and molecular archaeology. Various ancestry inferring methods have been released for major continental populations. However, few reports refer to sub-populations within the East Asian population using hundreds of ancestry informative SNPs (AISNPs). In this study, we developed a 308-AISNP panel (EASplex NGS DNA panel) using multiplex PCR and next generation sequencing (NGS). This panel included 56 SNPs relevant for the continent-level ancestry inference and 252 Japanese-, Korean-, and/or Han Chinese-specific AISNPs to address the ancestry inference of global populations and regional populations among Japanese (JPT), Korean minority (CHK), and Han Chinese (CHH). A total of 87 CHK and 59 CHH samples were used to check the performance of the EASplex NGS DNA panel. By analyzing 146 profiles of samples with JPT and CHH data from Beijing and South China in 1000 genomes project, the following results were obtained: (1) the 146 tested samples were correctly assigned to the East Asian group; (2) the paired population assignment rate was 99.73% for JPT and CHH, 95% for JPT and CHK, and 90.11% for CHK and CHH; and (3) the whole population assignment was 92.14% for the JPT, CHK, and CHH data. Overall, the EASplex NGS DNA panel displayed informativeness for continental ancestry inference and regional ancestry inference among JPT, CHH, and CHK and has the potential for use in forensic and genetic population studies.


      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


        • Phillips C.
        • Salas A.
        • Sánchez J.J.
        • et al.
        Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs.
        Forensic Sci. Int.: Genet. 2007; 1: 273-280
        • Kidd K.K.
        • Speed W.C.
        • Pakstis A.J.
        • et al.
        Progress toward an efficient panel of SNPs for ancestry inference.
        Forensic Sci. Int.: Genet. 2014; 10: 23-32
        • Kosoy R.
        • Nassir R.
        • Tian C.
        • et al.
        Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America.
        Hum. Mutat. 2009; 30: 69-78
        • Wei Y.-L.
        • Wei L.
        • Zhao L.
        • et al.
        A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents.
        Int. J. Leg. Med. 2015; 130: 27-37
        • Phillips C.
        • McNevin D.
        • Kidd K.K.
        • et al.
        Maplex - a massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations.
        Forensic Sci. Int.: Genet. 2019; 42: 213-226
        • Santos C.
        • Phillips C.
        • Fondevila M.
        • et al.
        Pacifiplex: An ancestry-informative SNP panel centred on Australia and the Pacific region.
        Forensic Sci. Int.: Genet. 2016; 20: 71-80
        • Yahya P.
        • Sulong S.
        • Harun A.
        • et al.
        Analysis of the genetic structure of the Malay population: Ancestry-informative marker SNPs in the Malay of Peninsular Malaysia.
        Forensic Sci. Int.: Genet. 2017; 30: 152-159
        • Phillips C.
        • Aradas A.F.
        • Kriegel A.K.
        • et al.
        Eurasiaplex: A forensic SNP assay for differentiating European and South Asian ancestries.
        Forensic Sci. Int.: Genet. 2013; 7: 359-366
        • Truelsen D.
        • Pereira V.
        • Phillips C.
        • et al.
        Evaluation of a custom GeneReadTM massively parallel sequencing assay with 210 ancestry informative SNPs using the ion S5TM and MiSeq platforms.
        Forensic Sci. Int.: Genet. 2021; 50102411
        • Warshauer D.H.
        • Davis C.P.
        • Holt C.
        • et al.
        Massively parallel sequencing of forensically relevant single nucleotide polymorphisms using TruSeqTM forensic amplicon.
        Int. J. Leg. Med. 2015; 129: 31-36
        • Wang Y.
        • Lu D.
        • Chung Y.-J.
        • et al.
        Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations.
        Hereditas. 2018; 155
        • Stoneking M.
        • Delfin F.
        The human genetic history of East Asia: weaving a complex tapestry.
        Curr. Biol. 2010; 20: R188-R193
        • Kim J.-J.
        • Verdu P.
        • Pakstis A.J.
        • et al.
        Use of autosomal loci for clustering individuals and populations of East Asian origin.
        Hum. Genet. 2005; 117: 511-519
        • Li C.-X.
        • Pakstis A.J.
        • Jiang L.
        • et al.
        A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia.
        Forensic Sci. Int.: Genet. 2016; 23: 101-110
        • Shi C.M.
        • Liu Q.
        • Zhao S.
        • et al.
        Ancestry informative SNP panels for discriminating the major East Asian populations: Han Chinese, Japanese and Korean.
        Ann. Hum. Genet. 2019; 83: 348-354
        • Yuasa I.
        • Akane A.
        • Yamamoto T.
        • et al.
        Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles.
        Leg. Med. 2018; 33: 17-22
        • Jung J.Y.
        • Kang P.-W.
        • Kim E.
        • et al.
        Ancestry informative markers (AIMs) for Korean and other East Asian and south east asian populations.
        Int. J. Leg. Med. 2019; 133: 1711-1719
        • Robinson J.T.
        • Thorvaldsdóttir H.
        • Winckler W.
        • et al.
        Integrative genomics viewer.
        Nat. Biotechnol. 2011; 29: 24-26
        • Peakall R.
        • Smouse P.E.
        GenAIEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research--an update.
        Bioinformatics. 2012; 28: 2537-2539
        • Pritchard J.K.
        • Stephens M.
        • Donnelly P.
        Inference of population structure using multilocus genotype data.
        Genetics. 2000; 155: 945-959
        • 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
        • Truelsen D.
        • Freire-Aradas A.
        • Nazari M.
        • et al.
        Evaluation of a custom QIAseq targeted DNA panel with 164 ancestry informative markers sequenced with the illumina MiSeq.
        Sci. Rep. 2021; 11
      1. Infinium Asian screening array + multidisease -24, product brochure by Illumina.
        • Tian C.
        • Kosoy R.
        • Lee A.
        • et al.
        Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays.
        PLoS One. 2008; 3
        • Jeon S.
        • Bhak Y.
        • Choi Y.
        • et al.
        Korean Genome Project:1094 Korean personal genomes with clinical information.
        Sci. Adv. 6(eaaz7835). 2020;
        • Zhang P.
        • Luo H.
        • Li Y.
        • et al.
        NyuWa Genome esource: A deep whole-genome sequencing-based variation profile and reference panel for the Chinese population.
        Cell Rep. 2021; 37110017