Advertisement

Investigating the resolution of ancestry testing in geographic regions characterized by high population admixture

Published:September 19, 2019DOI:https://doi.org/10.1016/j.fsigss.2019.09.005

      Abstract

      Ancestry testing can provide valuable information in forensic applications, but its efficiency has not yet been properly evaluated when used in highly admixed populations. In this work we tested a commercial ancestry panel containing 165 autosomal SNPs in 30 Dubai residents. Most of the tested individuals displayed, as expected, an admixed profile, but in general the main inferred ancestry was of Southwest Asian extraction, testifying that these tests can provide useful complementary forensic information.

      Keywords

      1. Introduction

      We have been conducting several genomic studies across the Arabian Peninsula, confirming it is a melting pot of the three main ancestries, African, Eurasian and East Asian [
      • Alshamali F.
      • Pereira L.
      • Budowle B.
      • Poloni E.S.
      • Currat M.
      Local population structure in Arabian Peninsula revealed by Y-STR diversity.
      ,
      • Fernandes V.
      • Alshamali F.
      • Alves M.
      • Costa M.D.
      • Pereira J.B.
      • Silva N.M.
      • Cherni L.
      • Harich N.
      • Cerny V.
      • Soares P.
      • Richards M.B.
      • Pereira L.
      The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa.
      ,
      • Fernandes V.
      • Triska P.
      • Pereira J.B.
      • Alshamali F.
      • Rito T.
      • Machado A.
      • Fajkošová Z.
      • Cavadas B.
      • Černý V.
      • Soares P.
      • Richards M.B.
      • Pereira L.
      Genetic stratigraphy of key demographic events in Arabia.
      ,
      • Fernandes V.
      • Brucato N.
      • Ferreira J.C.
      • Pedro N.
      • Cavadas B.
      • Ricaut F.X.
      • Alshamali F.
      • Pereira L.
      Genome-wide characterization of Arabian Peninsula populations: shedding light on the history of a fundamental bridge between continents.
      ]. The admixture has been taking place since pre-historic times, and attained an astounding dimension at contemporary times in places such as the United Arab Emirates (UAE) where the non-native population amounts to ∼80%. This phenomenon challenges the use of ancestry testing in forensic genetics, which could provide additional information on a suspect or strengthen eyewitness accounts. It is thus important to evaluate the level of resolution that these tests provide when applied in the context of migration nexus such as UAE. In this work, we performed the genotyping of the Applied Biosystems™ Precision ID Ancestry Panel (Applied Biosystems, Foster City, California, United States of America), containing 165 autosomal SNPs that can provide biogeographic ancestry information.

      2. Methods

      We performed the genotyping of the Applied Biosystems™ Precision ID Ancestry Panel (Thermo Fisher, Waltham, MA, USA) in 30 residents in Dubai, the UAE, born in different countries: 21 UAE, 2 Yemeni, 1 Saudi, 1 Omani, 1 Iranian, 1 Pakistani, 1 Ethiopian, 1 Sudanese and 1 Egyptian. Samples were quantified using Qubit dsDNA HS Assay Kit and normalized to 1 ng in 15 μl. SNP libraries were constructed using Ion AmpliSeq Kit for Chef DL8 with Precision ID Ancestry Panel on the Ion Chef instrument and with 22 PCR cycles as per the manufacturer’s recommendations. The chef prepared pooled libraries were then diluted to an equimolar concentration of 30 pM for template preparation. Template preparation, enrichment of beads containing template and chip loading of the templated beads on Ion 530 chip were performed using the Ion Chef instrument and the Ion S5 Precision ID Chef & Sequencing Kit as instructed in the manual. Sequencing was done on an Ion S5 NGS with the Torrent Suite Software v5.2.2 and with default settings using Hg 19 as the reference genome. Data analyses were performed using the HID SNP Genotyper Plugin.

      3. Results and discussion

      The inferred ancestry (Table 1) showed a very diverse profile of admixture. Only three Arabians showed a 100% Southwest Asian (SWA) profile, 16 of them showed a main SWA proportion (between 40% and 90%) admixed with one or two other ancestries, while the remaining six were highly admixed. Even so, all the Arabian individuals were mapped around SWA. The Egyptian profile resembled a low admixed Arabian (95% SWA), while the Iranian had European (60%) added by SWA (30%) components. The Pakistani had the highest South Asian profile (70%), mixed with three other ancestries. The two Africans were also admixed: the Ethiopian had 45% African and 55% SWA; while the Sudanese had 30% and 70%, respectively of those ancestries. The top most inferred population is highly dependent on the populations included as reference in the software, and this type of information should be dealt with great caution.
      Table 1Inferred admixture proportions and top most inferred population and geographical region of the 30 samples from UAE residents by genotyping the Applied Biosystems™ Precision ID Ancestry Panel (Panel (Thermo Fisher, Waltham, MA, USA).
      Inferred admixture proportions
      Sample IDNationality of originAfricaEuropeSouthwest AsiaSouth AsiaEast AsiaOceaniaAmericaTop most inferred populationInferred RegionLikelihood
      UAE_1UAE0%20%80%0%0%0%0%Jews, YemeniteAsia1.13E-44
      UAE_2UAE20%25%45%0%0%0%10%Negroid makraniAsia2.06E-56
      UAE_3UAE0%0%100%0%0%0%0%PalestinianAsia8.63E-47
      UAE_4UAE5%0%45%45%0%5%0%MohannaAsia1.61E-50
      UAE_5UAE0%20%35%45%0%0%0%KeraliteAsia1.20E-43
      UAE_6UAE0%10%55%35%0%0%0%PashtunAsia8.95E-45
      UAE_7UAE5%0%60%35%0%0%0%Negroid makraniAsia7.33E-48
      UAE_8UAE0%0%70%10%5%15%0%PashtunAsia2.52E-51
      UAE_9UAE0%20%55%25%0%0%0%KuwaitiAsia5.50E-48
      UAE_10UAE0%25%75%0%0%0%0%SardinianAsia3.45E-40
      UAE_11UAE15%0%85%0%0%0%0%Negroid MakraniAsia7.50E-47
      UAE_12UAE20%0%80%0%0%0%0%Negroid MakraniAsia2.32E-52
      UAE_13UAE25%5%20%50%0%0%0%Negroid MakraniAsia2.60E-48
      UAE_14UAE0%15%65%20%0%0%0%AdygeiEurope6.19E-47
      UAE_15UAE0%15%85%0%0%0%0%KuwaitiAsia3.21E-44
      UAE_16UAE5%30%10%55%0%0%0%MohannaAsia3.36E-48
      UAE_17UAE5%15%60%20%0%0%0%Negroid MakraniAsia4.35E-46
      UAE_18UAE0%45%40%0%0%15%0%PalestinianAsia4.63E-48
      UAE_19UAE30%0%45%25%0%0%0%Negroid MakraniAsia8.49E-50
      UAE_20UAE25%30%40%5%0%0%0%Negroid MakraniAsia3.03E-45
      UAE_21UAE0%0%100%0%0%0%0%KuwaitiAsia4.97E-37
      UAE_28Omani5%0%90%5%0%0%0%PalestinianAsia3.35E-45
      UAE_27Saudi0%15%80%5%0%0%0%PalestinianAsia1.54E-46
      UAE_22Yemen0%0%100%0%0%0%0%KuwaitiAsia1.21E-41
      UAE_23Yemen5%0%75%0%0%0%20%PalestinianAsia1.25E-56
      UAE_29Iran0%60%30%5%0%5%0%HungarianEurope3.70E-42
      UAE_25Pakistan10%0%0%70%15%5%0%KeraliteAsia3.04E-52
      UAE_26Egypt5%0%95%0%0%0%0%Jews, YemeniteAsia2.10E-45
      UAE_30Ethiopia45%0%55%0%0%0%0%SomaliAfrica7.39E-52
      UAE_24Sudan30%0%70%0%0%0%0%Jews, EthiopianAfrica1.44E-47

      4. Conclusions

      This work shows that the application of ancestry tests can be used to provide investigative leads to solve crimes, but values should not be strictly interpreted given the highly admixed profile of some populations, such as the UAE.

      Acknowledgements

      i3S is financed by FEDER - COMPETE 2020 and by Portuguese funds through FCT/Ministério da Ciência, Tecnologia e Inovação in the framework of the project “Institute for Research and Innovation in Health Sciences” (POCI-01-0145-FEDER-007274).

      References

        • Alshamali F.
        • Pereira L.
        • Budowle B.
        • Poloni E.S.
        • Currat M.
        Local population structure in Arabian Peninsula revealed by Y-STR diversity.
        Hum. Hered. 2009; 68: 45-54
        • Fernandes V.
        • Alshamali F.
        • Alves M.
        • Costa M.D.
        • Pereira J.B.
        • Silva N.M.
        • Cherni L.
        • Harich N.
        • Cerny V.
        • Soares P.
        • Richards M.B.
        • Pereira L.
        The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa.
        Am. J. Hum. Genet. 2012; 90: 347-355
        • Fernandes V.
        • Triska P.
        • Pereira J.B.
        • Alshamali F.
        • Rito T.
        • Machado A.
        • Fajkošová Z.
        • Cavadas B.
        • Černý V.
        • Soares P.
        • Richards M.B.
        • Pereira L.
        Genetic stratigraphy of key demographic events in Arabia.
        PLoS One. 2015; 10e0118625
        • Fernandes V.
        • Brucato N.
        • Ferreira J.C.
        • Pedro N.
        • Cavadas B.
        • Ricaut F.X.
        • Alshamali F.
        • Pereira L.
        Genome-wide characterization of Arabian Peninsula populations: shedding light on the history of a fundamental bridge between continents.
        Mol. Biol. Evol. 2019; 36: 575-586