Short Communication| Volume 16, P58-63, May 2015

Ancestry informative markers: Inference of ancestry in aged bone samples using an autosomal AIM-Indel multiplex

Published:December 05, 2014DOI:


      • We typed aged bone samples with ancestry informative 46 Indels kit.
      • Bone samples were collected from Sub-Saharan Africa, America, East Asia and Europe.
      • AIM Indels successfully estimated the proportion of ancestry of the aged samples.


      Ancestry informative markers (AIMs) can be useful to infer ancestry proportions of the donors of forensic evidence. The probability of success typing degraded samples, such as human skeletal remains, is strongly influenced by the DNA fragment lengths that can be amplified and the presence of PCR inhibitors. Several AIM panels are available amongst the many forensic marker sets developed for genotyping degraded DNA. Using a 46 AIM Insertion Deletion (Indel) multiplex, we analyzed human skeletal remains of post mortem time ranging from 35 to 60 years from four different continents (Sub-Saharan Africa, South and Central America, East Asia and Europe) to ascertain the genetic ancestry components. Samples belonging to non-admixed individuals could be assigned to their corresponding continental group. For the remaining samples with admixed ancestry, it was possible to estimate the proportion of co-ancestry components from the four reference population groups. The 46 AIM Indel set was informative enough to efficiently estimate the proportion of ancestry even in samples yielding partial profiles, a frequent occurrence when analyzing inhibited and/or degraded DNA extracts.


      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


        • Kersbergen P.
        • van Duijn K.
        • Kloosterman A.D.
        • den Dunnen J.T.
        • Kayser M.
        • de Knijff P.
        Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans.
        BMC Genet. 2009; 10: 69
        • Fondevila M.
        • Phillips C.
        • Santos C.
        • Freire Aradas A.
        • Vallone P.M.
        • Butler J.M.
        • Lareu M.V.
        • Carracedo A.
        Revision of the SNPforID 34-plex forensic ancestry test: assay enhancements, standard reference sample genotypes and extended population studies.
        Forensic Sci. Int. Genet. 2013; 7: 63-74
        • Shriver M.D.
        • Mei R.
        • Parra E.J.
        • Sonpar V.
        • Halder I.
        • Tishkoff S.A.
        • Schurr T.G.
        • Zhadanov S.I.
        • Osipova L.P.
        • Brutsaert T.D.
        • et al.
        Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation.
        Hum. Genomics. 2005; 2: 81-89
        • Lao O.
        • van Duijn K.
        • Kersbergen P.
        • de Knijff P.
        • Kayser M.
        Proportioning whole genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry.
        Am. J. Hum. Genet. 2006; 78: 680-690
        • Paschou P.
        • Ziv E.
        • Burchard E.G.
        • Choudhry S.
        • Rodriguez-Cintron W.
        • Mahoney M.W.
        • Drineas P.
        PCA-correlated SNPs for structure identification in world-wide human populations.
        PLoS Genet. 2007; 3: 1672-1686
        • Enoch M.A.
        • Shen P.H.
        • Xu K.
        • Hodgkinson C.
        • Goldman D.
        Using ancestry-informative markers to define populations and detect population stratification.
        J. Psychol. Pharmacol. 2006; 20: 19-26
        • Phillips C.
        • Salas A.
        • Sanchez J.J.
        • Fondevila M.
        • Gomez-Tato A.
        • Alvarez-Dios J.
        • Calaza M.
        • de Cal M.C.
        • et al.
        Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs.
        Forensic Sci. Int. Genet. 2007; 1: 273-280
        • Kidd J.R.
        • Friedlaender F.R.
        • Speed W.C.
        • Pakstis A.J.
        • De La Vega F.M.
        • Kidd K.K.
        Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples.
        Invest. Genet. 2011; 2: 1
        • Phillips C.
        • Parson W.
        • Lundsberg B.
        • Santos C.
        • Freire-Aradas A.
        • Torres M.
        • Eduardoff M.
        • Børsting C.
        • et al.
        Building a forensic ancestry panel from the ground up: the EUROFORGEN Global AIM-SNP set.
        Forensic Sci. Int. Genet. 2014; 11: 13-25
        • Phillips C.
        • Freire Aradas A.
        • Kriegel A.K.
        • Fondevila M.
        • Bulbul O.
        • Santos C.
        • Serrulla Rech F.
        • Perez Carceles M.D.
        • et al.
        Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries.
        Forensic Sci. Int. Genet. 2013; 7: 359-366
        • Mullaney J.M.
        • Mills R.E.
        • Pittard W.S.
        • Devine S.E.
        Small insertions and deletions (INDELs) in human genomes.
        Hum. Mol. Genet. 2010; 19: R131-R136
        • Pereira R.
        • Phillips C.
        • Pinto N.
        • Santos C.
        • de Santos S.E.
        • et al.
        Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing.
        PLoS ONE. 2012; 7: e29684
        • Sanchez J.J.
        • Phillips C.
        • Børsting C.
        • Balogh K.
        • Bogus M.
        • Fondevila M.
        • Harrison C.D.
        • Musgrave-Brown E.
        • et al.
        A multiplex assay with 52 single nucleotide polymorphisms for human identification.
        Electrophoresis. 2006; 27: 1713-1724
        • Pereira R.
        • Phillips C.
        • Alves C.
        • Amorim A.
        • Carracedo A.
        • et al.
        A new multiplex for human identification using insertion/deletion polymorphisms.
        Electrophoresis. 2009; 30: 3682-3690
        • Phillips C.
        • Fondevila M.
        • Lareu M.V.
        A 34-plex autosomal SNP single base extension assay for ancestry investigations.
        Methods Mol. Biol. 2012; 830: 109-126
        • Alaeddini R.
        Forensic implications of PCR inhibition: a review.
        Forensic Sci. Int. Genet. 2012; 6: 297-305
        • Alaeddini R.
        • Walsh S.J.
        • Abbas A.
        Forensic implications of genetic analysis from degraded DNA: a review.
        Forensic Sci. Int. Genet. 2010; 4: 149-157
        • Fondevila M.
        • Phillips C.
        • Naveran N.
        • Fernandez L.
        • Cerezo M.
        • Salas A.
        • Carracedo A.
        • Lareu M.V.
        Case report: identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur.
        Forensic Sci. Int. Genet. 2008; 2: 212-218
        • Romanini C.
        • Catelli M.L.
        • Borosky A.
        • Pereira R.
        • Romero M.
        • Salado Puerto M.
        • Phillips C.
        • et al.
        Typing short amplicon binary polymorphisms: supplementary SNP and Indel genetic information in the analysis of highly degraded skeletal remains.
        Forensic Sci. Int. Genet. 2012; 6: 469-476
      1. Latin American Initiative for the Identification of the “Disappeared” (LIID), Argentinean Forensic Anthropology Team (EAAF).

        • Carracedo A.
        • Bär W.
        • Lincoln P.
        • Mayr W.
        • Morling N.
        • Olaisen B.
        • Schneider P.
        • Budowle B.
        • et al.
        DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing.
        Forensic Sci. Int. Genet. 2000; 110: 79-85
        • Pritchard J.K.
        • Stephens M.
        • Donnelly P.
        Inference of population structure using multilocus genotype data.
        Genetics. 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
        • Cann H.M.
        • de Toma C.
        • Cazes L.
        • Legrand M.F.
        • Morel V.
        • et al.
        A human genome diversity cell line panel.
        Science. 2002; 296: 261-262
        • Rosenberg N.A.
        Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives.
        Ann. Hum. Genet. 2006; 70: 841-847
        • Santos N.P.
        • Ribeiro-Rodrigues E.M.
        • Ribeiro-dos-Santos A.K.
        • Pereira R.
        • Gusmão L.
        • et al.
        Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INDEL) ancestry informative marker (AIM) panel.
        Hum. Mut. 2010; 31: 184-190
        • Toscanini U.
        • Gusmão L.
        • Berardi G.
        • Gómez A.
        • Pereira R.
        • Raimondi E.
        Ancestry proportions in urban populations of Argentina.
        Forensic Sci. Int. Genet. Suppl. Ser. 2011; 3: 387-388
        • Heinz T.
        • Alvarez-Iglesias V.
        • Pardo-Seco J.
        • Taboada-Echalar P.
        • Gomez-Carballa A.
        • Torres-Balanza A.
        • Rocabado O.
        • Carracedo A.
        • Vullo C.
        • Salas A.
        Ancestry analysis reveals a predominant Native American component with moderate European admixture in Bolivians.
        Forensic Sci. Int. Genet. 2013; 7: 537-542