Advertisement

Ancestry resolution of South Brazilians by forensic 165 ancestry-informative SNPs panel

  • Aline Brugnera Felkl
    Correspondence
    Correspondence to: Laboratório de Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul. Av. Ipiranga, 6681, 90619-900, Prédio 12C, Sala 233, Porto Alegre, RS, Brazil.
    Affiliations
    Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil

    National Institute of Science and Technology – Forensic Science, Porto Alegre, RS, Brazil
    Search for articles by this author
  • Eduardo Avila
    Affiliations
    Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil

    Technical Scientific Section, Federal Police Department in Rio Grande do Sul State, Porto Alegre, RS, Brazil

    National Institute of Science and Technology – Forensic Science, Porto Alegre, RS, Brazil
    Search for articles by this author
  • André Zoratto Gastaldo
    Affiliations
    Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil

    National Institute of Science and Technology – Forensic Science, Porto Alegre, RS, Brazil
    Search for articles by this author
  • Catieli Gobetti Lindholz
    Affiliations
    Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil
    Search for articles by this author
  • Márcio Dorn
    Affiliations
    Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil

    National Institute of Science and Technology – Forensic Science, Porto Alegre, RS, Brazil

    Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
    Search for articles by this author
  • Clarice Sampaio Alho
    Affiliations
    Forensic Genetics Laboratory, School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil

    National Institute of Science and Technology – Forensic Science, Porto Alegre, RS, Brazil
    Search for articles by this author
Published:January 23, 2023DOI:https://doi.org/10.1016/j.fsigen.2023.102838

      Highlights

      • 250 samples from four South Brazilian population groups were typed for 165 AISNPs.
      • All loci were in HW equilibrium, with association between seven loci pairs.
      • South Amerindians show greater miscegenation than European-derived Gauchos.
      • Admixed and African-derived present the highest levels of population stratification.
      • The panel is a promising tool for biogeographical ancestry and human identification.

      Abstract

      Forensic DNA phenotyping (FDP) includes biogeographic ancestry (BGA) inference and externally visible characteristics (EVCs) prediction directly from an evidential DNA sample as alternatives to provide valuable intelligence when conventional DNA profiling fails to achieve identification. In this context, the application of Massively Parallel Sequencing (MPS) methodologies, which enables simultaneous typing of multiple samples and hundreds of forensic markers, has been gradually implemented in forensic genetic casework. The Precision ID Ancestry Panel (Thermo Fisher Scientific, Waltham, USA) is a forensic multiplex assay consisting of 165 autosomal SNPs designed to provide biogeographic ancestry information. In this work, a sample of 250 individuals from Rio Grande do Sul (RS) State, southern Brazil, apportioned into four main population groups (African-, European-, Amerindian-, and Admixed-derived Gauchos), was evaluated with this panel, to assess the feasibility of this approach in a highly heterogeneous population. Forensic descriptive parameters estimated for each population group revealed that this panel has enough polymorphic and informative SNPs to be used as a supplementary instrument in forensic individual identification and kinship testing regardless of ethnicity. No statistically significant deviation from Hardy-Weinberg equilibrium was observed after Bonferroni correction. However, seven loci pairs displayed linkage disequilibrium in pairwise LD testing (p < 3.70 × 10-6). Interpopulation comparisons by FST analysis, MDS plot, and STRUCTURE analysis among the four RS population groups apart and along with 89 reference worldwide populations demonstrated that Admixed- and African-derived Gauchos present the highest levels of admixture and population stratification, whereas European- and Amerindian-derived exhibit a more homogeneous genetic conformation.

      Keywords

      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:

      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

      References

        • Kayser M.
        Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes.
        Forensic Sci Int Genet. 2015; 18: 33-48
        • Kayser M.
        • De Knijff P.
        Improving human forensics through advances in genetics, genomics and molecular biology.
        Nat Rev Genet. 2011; 12: 179-192
        • Phillips C.
        Forensic genetic analysis of bio-geographical ancestry.
        Forensic Sci Int Genet. 2015; 18: 49-65
        • Børsting C.
        • Morling N.
        Next generation sequencing and its applications in forensic genetics.
        Forensic Sci Int Genet. 2015; 18: 78-89
        • Bruijns B.
        • Tiggelaar R.
        • Gardeniers H.
        Massively parallel sequencing techniques for forensics: A review.
        Electrophoresis. 2018; 39: 2642-2654
        • 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
        • Salzano F.M.
        • Sans M.
        Interethnic admixture and the evolution of Latin American populations.
        Genet Mol Biol. 2014; 37: 151-170
        • Moura R.R.
        • Coelho A.V.
        • Balbino V.
        • Crovella S.
        • Brandão L.A.
        Meta-analysis of Brazilian genetic admixture and comparison with other Latin America countries.
        Am J Hum Biol. 2015; 27: 674-680
        • Curtin P.D.
        The Atlantic slave trade: A census.
        University of Wisconsin Press, Madison, WI1969
        • Callegari-Jacques S.M.
        • Grattapaglia D.
        • Salzano F.M.
        • et al.
        Historical genetics: spatiotemporal analysis of the formation of the Brazilian population.
        Am J Hum Biol. 2003; 15: 824-834
        • IBGE
        Brasil: 500 anos de povoamento.
        Instituto Brasileiro de Geografia e Estatística, Rio de Janeiro2007
        • Pena S.D.
        • Di Pietro G.
        • Fuchshuber-Moraes M.
        • et al.
        The genomic ancestry of individuals from different geographical regions of Brazil is more uniform than expected.
        PLoS One. 2011; 6e17063
        • Marrero A.R.
        • Bravi C.
        • Stuart S.
        • et al.
        Pre- and post-Columbian gene and cultural continuity: the case of the Gaucho from southern Brazil.
        Hum Hered. 2007; 64: 160-171
        • Gouveia M.H.
        • Borda V.
        • Leal T.P.
        • et al.
        Origins, admixture dynamics and homogenization of the African gene pool in the Americas.
        Mol Biol Evol. 2020; 1;37: 1647-1656
        • World Medical Association
        World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects.
        JAMA. 2013; 310: 2191-2194
      1. Thermo Fisher Scientific. Ion PGM™ Hi-Q™ OT2 Kit. Revision A.0 ( 2015 ). Waltham, MA, USA.

      2. Thermo Fisher Scientific. Ion PGM™ Hi-Q™ Sequencing Kit. Revision C.0 ( 2015 ). Waltham, MA, USA.

      3. Illumina. AmpliSeq for Illumina On-Demand, Custom, and Community Panels. Document # 1000000036408 v08 ( 2019 ). San Diego, CA, USA.

      4. Illumina. MiSeq System: Denature and Dilute Libraries Guide. Document # 15039740 v10 ( 2019 ). San Diego, CA, USA.

        • Eduardoff M.
        • Santos C.
        • de la Puente M.
        • et al.
        Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™.
        Forensic Sci Int Genet. 2015; 17: 110-121
        • Avila E.
        • Cavalheiro C.P.
        • Felkl A.B.
        • et al.
        Brazilian forensic casework analysis through MPS applications: Statistical weight-of-evidence and biological nature of criminal samples as an influence factor in quality metrics.
        Forensic Sci Int. 2019; 303109938
        • Wasik K.
        • Berisa T.
        • Pickrell J.K.
        • et al.
        Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics.
        BMC Genomic. 2021; 20;22: 197
        • Li N.
        • Stephens M.
        Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
        Genetics. 2003; 165: 2213-2233
        • Lischer H.E.
        • Excoffier L.
        PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs.
        Bioinformatics. 2012; 28: 298-299
        • Gouy A.
        • Zieger M.
        STRAF - A convenient online tool for STR data evaluation in forensic genetics.
        Forensic Sci Int Genet. 2017; 30: 148-151
        • Excoffier L.
        • Lischer H.E.
        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
        • Bonferroni C.E.
        Teoria statistica delle classi e calcolo delle probabilità.
        Pubblicazioni del Regio Istituto Superiore di Scienze Economiche e Commerciali di Firenze. 1936; 8: 3-62
        • Abecasis G.R.
        • Auton A.
        • et al.
        • 1000 Genomes Project Consortium
        An integrated map of genetic variation from 1,092 human genomes.
        Nature. 2012; 491: 56-65
        • García O.
        • Ajuriagerra J.A.
        • Alday A.
        • et al.
        Frequencies of the precision ID ancestry panel markers in Basques using the Ion Torrent PGMTM platform.
        Forensic Sci Int Genet. 2017; 31: e1-e4
        • He G.
        • Wang Z.
        • Wang M.
        • et al.
        Forensic ancestry analysis in two Chinese minority populations using massively parallel sequencing of 165 ancestry-informative SNPs.
        Electrophoresis. 2018; 39: 2732-2742
        • 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
        • Pakstis A.J.
        • Speed W.C.
        • Soundararajan U.
        • et al.
        Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels.
        Sci Rep. 2019; 9: 18874
      5. I.B.M. Corp . I.B.M. SPSS Statistics for Windows. Version 25.0, Released 2017 . Armonk, NY.

        • 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
        • Kopelman N.M.
        • Mayzel J.
        • Jakobsson M.
        • Rosenberg N.A.
        • Mayrose I.
        Clumpak: a program for identifying clustering modes and packaging population structure inferences across K.
        Mol Ecol Resour. 2015; 15: 1179-1191
        • 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
        • Nakanishi H.
        • Pereira V.
        • Børsting C.
        • et al.
        Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel.
        Forensic Sci Int Genet. 2018; 33: 106-109
        • Wang Z.
        • He G.
        • Luo T.
        • et al.
        Massively parallel sequencing of 165 ancestry informative SNPs in two Chinese Tibetan-Burmese minority ethnicities.
        Forensic Sci Int Genet. 2018; 34: 141-147
        • Simayijiang H.
        • Børsting C.
        • Tvedebrink T.
        • Morling N.
        Analysis of Uyghur and Kazakh populations using the Precision ID Ancestry Panel.
        Forensic Sci Int Genet. 2019; 43102144
        • Xie T.
        • Shen C.
        • Liu C.
        • et al.
        Ancestry inference and admixture component estimations of Chinese Kazak group based on 165 AIM-SNPs via NGS Platform.
        J Hum Genet. 2020;
        • Lee J.H.
        • Cho S.
        • Kim M.Y.
        • et al.
        Genetic resolution of applied biosystems™ precision ID Ancestry panel for seven Asian populations.
        Leg Med (Tokyo). 2018; 34: 41-47
        • Espregueira Themudo G.
        • Smidt Mogensen H.
        • Børsting C.
        • Morling N.
        Frequencies of HID-ion ampliseq ancestry panel markers among greenlanders.
        Forensic Sci Int Genet. 2016; 24: 60-64
        • Santangelo R.
        • González-Andrade F.
        • Børsting C.
        • Torroni A.
        • Pereira V.
        • Morling N.
        Analysis of ancestry informative markers in three main ethnic groups from Ecuador supports a trihybrid origin of Ecuadorians.
        Forensic Sci Int Genet. 2017; 31: 29-33
        • Truelsen D.M.
        • Farzad M.S.
        • Mogensen H.S.
        • et al.
        Typing of two Middle Eastern populations with the Precision ID Ancestry Panel.
        Forensic Sci Int Genet. 2017; 6: e301-e302
      6. IBGE. Sistema IBGE de Recuperação Automática - SIDRA. Tabela 136 - População residente por cor ou raça ( 2010 ). Instituto Brasileiro de Geografia e Estatística.

      7. IBGE. Brasil: 500 anos de povoamento ( 2007 ). Rio de Janeiro: Instituto Brasileiro de Geografia e Estatística.

        • Phillips C.
        • Ballard D.
        • Gill P.
        • Court D.S.
        • Carracedo A.
        • Lareu M.V.
        The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP data.
        Forensic Sci Int Genet. 2012; 6: 354-365
        • Ardlie K.G.
        • Kruglyak L.
        • Seielstad M.
        Patterns of linkage disequilibrium in the human genome.
        Nat Rev Genet. 2002; 3: 299-309
        • Saloum de Neves Manta F.
        • Pereira R.
        • Vianna R.
        • et al.
        Revisiting the genetic ancestry of Brazilians using autosomal AIM-Indels.
        PLoS One. 2013; 8e75145
        • Parra F.C.
        • Amado R.C.
        • Lambertucci J.R.
        • Rocha J.
        • Antunes C.M.
        • Pena S.D.
        Color and genomic ancestry in Brazilians.
        Proc Natl Acad Sci U S A. 2003; 100: 177-182
        • Pena S.D.
        • Di Pietro G.
        • Fuchshuber-Moraes M.
        • et al.
        The genomic ancestry of individuals from different geographical regions of Brazil is more uniform than expected.
        PLoS One. 2011; 6e17063
        • Muniz Y.C.
        • Ferreira L.B.
        • Mendes-Junior C.T.
        • Wiezel C.E.
        • Simões A.L.
        Genomic ancestry in urban Afro-Brazilians.
        Ann Hum Biol. 2008; 35: 104-111
        • Gontijo C.C.
        • Mendes F.M.
        • Santos C.A.
        • et al.
        Ancestry analysis in rural Brazilian populations of African descent.
        Forensic Sci Int Genet. 2018; 36: 160-166
        • Avila E.
        • Felkl A.B.
        • Graebin P.
        • Nunes C.P.
        • Alho C.S.
        Forensic characterization of Brazilian regional populations through massive parallel sequencing of 124 SNPs included in HID ion Ampliseq Identity Panel.
        Forensic Sci Int Genet. 2019; 40: 74-84
      8. I.B.G.E. . Sistema IBGE de Recuperação Automática - SIDRA. Tabela 136 - População residente por cor ou raça ( 2010 ). Instituto Brasileiro de Geografia e Estatística.

        • Pimenta J.R.
        • Zuccherato L.W.
        • Debes A.A.
        • et al.
        Color and genomic ancestry in Brazilians: a study with forensic microsatellites.
        Hum Hered. 2006; 62: 190-195
        • Moriot A.
        • Santos C.
        • Freire-Aradas A.
        • Phillips C.
        • Hall D.
        Inferring biogeographic ancestry with compound markers of slow and fast evolving polymorphisms.
        Eur J Hum Genet. 2018; 26: 1697-1707
        • Pakstis A.J.
        • Gurkan C.
        • Dogan M.
        • et al.
        Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs.
        Eur J Hum Genet. 2019; 27: 1885-1893