Review of biogeographical ancestry markers and their application to forensic investigation

Authors

  • Daniela María Popa Universidad Complutense de Madrid
  • Eduardo Arroyo Pardo Universidad Complutense de Madrid
  • Ana María López Parra Universidad Complutense de Madrid

DOI:

https://doi.org/10.16925/cf.v4i1.1958

Keywords:

InDels, biogeographic ancestry, snp, str

Abstract

Purpose: The markers that determine biogeographical ancestry are booming, especially in the forensic field. These markers allow to analyze the dna of an individual and determine their biogeographical origin. These analyses are carried out frequently through SNP (Single Nucleotide Polymorphisms), but more recently through InDels as well. Because of this boom, the purpose of the review is to gather information about the markers currently being used, their different performance and their problems, as well as possible solutions. Period covered, origin and types of publications: The period covered for the analysis is 2006-2016, compiling articles from PubMed and Web of Science, with no preference as to origin.Point of view: Although they have been used for different populations and with different markers, they show similar results. Articles range from the types of markers selected for analysis, such as autosomal or lineage markers, to comparisons among markers in the same category, such as SNPS and InDels among autosomal ones. They have been thus selected to obtain a comparative view of the most effective for the detection of biogeographical ancestry. Conclusions: The most effective markers are autosomal AIM-SNP, in terms of differentiation among population groups, and supplementary AIM-InDels, in cases of population mixing.

Author Biographies

Daniela María Popa, Universidad Complutense de Madrid

Laboratorio de Genética Forense, Dpto de Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid España.

Eduardo Arroyo Pardo, Universidad Complutense de Madrid

Laboratorio de Genética Forense, Dpto de Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid España.

Ana María López Parra, Universidad Complutense de Madrid

Laboratorio de Genética Forense. Dpto. de Toxicología y Legislación Sanitaria. Facultad de Medicina. Universidad Complutense de Madrid. Madrid. España

References

Phillips C. Forensic genetic analysis of bio-geographical ancestry. Forensic Sci. Int. Genet. 2015;18: 49-65.

Rosenberg N, Pritchard J, Weber J, Cann H, Kidd K, Zhivotovsky L, et al. Genetic Structure of Human Populations. Science. 2002;298: 2381-2385.

Lareu Huidobro V. Nuevos polimorfismos de ADN: prediccion de origen biogeográfico y caracteristicas fisicas. En Casado M, Guillén M. ADN forense: Problemas éticos y jurídicos. Barcelona: Universidad de Barcelona; 2014; p. 157-168.

Bulbul O, Filoglul G, Zorlul T, Altuncull H, Freire-Aradas A, Söchtig J, et al. Inference of biogrographical ancestry across central regions of Eurasia. Int. J. Legal Med. 2016;130(1): 73-79.

Pardo-Secol J, Martinón-Torres F, Salas A. Evaluating the acurracy of AIM panels at quantifying genome ancestry. BMC Genomics. 2014;15: 543.

Halder I, Shriver M, Thomas M, Fernandez JR, Frudakis T. A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications. Hum. Mutat. 2008;29: 648-658.

Frudakis T. Molecular Photofitting. Predicting ancestry and phenotype using DNA. Elsevier Inc., British Library Cataloguing-in-Publication Data; 2008.

Phillips C, Salas A, Sánchez J, Fondevila M, Gómez-Tato A, Álvarez-Dios J, et al. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci. Int. Genet. 2007;1: 273-280.

Taboada-Echalar P, Álvarez-Iglesias V, Heinz T, Vidal-Bralo L, Gómez-Carballa A, Catelli L, Pardo-Seco J, Pastoriza A, Carracedo Á et al The genetic legacy of the pre-colonial period in contemporary Bolivians. PLoS One 2013;8: e58980.

Galanter JM, Fernandez-Lopez JC, Gignoux CR, Barnholtz-Sloan J, Fernandez-Rozadilla C, Via M, Hidalgo-Miranda A, Contreras AV, Uribe Figueroa L et al. Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas. PLoS Genet. 2012;8: e1002554.

Ruiz Orozco Y. FDP: "Forensic DNA Phenotyping". Aplicaciones de marcadores geneticos en la inferencia de características visibles externas y origen ancestral con fines forenses. Santiago de Compostela: Universidad Santiago de Compostela; 2012.

Butler JM, Coble MD, Vallone PM. STRa vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci. Med. Pathol. 2007;3: 200-205.

Fondevila M, Phillips C, Lareu M. Aplicaciones no convencionales de marcadores bialélicos (SNPs) en genética forense. Boletín Galego de Medicina Legal e Forense. 2014; 20.

Phillips C, Fernandez-Formoso L, Gelabert-Besada M, Garcia-Magariños M, Santos C, Fondevila M, et al. Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing. Electrophoresis. 2013;34(8): 1151-1162.

Graydon M, Cholette F, Ng LK. Inferring ethnicity using 15 autosomal STR loci--comparisons among populations of similar and distinctly different physical traits. Forensic Sci. Int. Genet. 2009;3(4): 251–254.

Pereira R, Phillips C, Pinto N, Santos C, Santos S, Amorim A, et al. Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS ONE. 2012;7(1): e29684.

Fondevila M, Phillips C, Santos C, Pereira R, Gusmao L, Carracedo A, et al. Forensic performance of two insertion-deletion marker assays. Int. J. Legal Med. 2012;126(5): 725-737.

Santos C, Phillips C, Oldoni F, Amigo J, Fondevila M, Pereira R, et al. Completion of a worldwide reference panel of samples for an ancestry informative Indel assay. Forensic Sci. Int. Genet. 2015;17: 75-80.

Fondevila M, Phillips C, Santos C, Freire-Aradas A, Vallone P, Butler J, et al. 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.

Laan M, Wiebe V, Khusnutdinova E, Remm M, Pääbo S. X-chromosome as a marker for population history: linkage desequilibrium and haplotype study in Eurasian populations. Eur. J. Hum. Genet. 2005;13(4): 452-462.

Ibarra A, Restrepo T, Rojas W, Castillo A, Amorim A, Martínez B, et al. Evaluating the X Chromosome- specific diversity of colombian population using insertion/deletion polymorphism. PLoS ONE. 2014;9(1): e87202.

Fan GY, Ye Y, Hou YP. Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome. Sci. Rep. 2016;6: 32178.

Rosenberg N, Li L, Ward R, Pritchard J. Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet. 2003;73: 1402-1422.

Eduardoff M, Gross TE, Santos C, de la Puente M, Ballard D, Strobl C, Børsting C, Morling N, Fusco L, Hussing C, Egyed B, Souto L, Uacyisrael J, Syndercombe Court D, Carracedo Á, Lareu MV, Schneider PM, Parson W, Phillips C; EUROFORGEN-NoE Consortium., Parson W, Phillips C. Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM. Forensic Sci. Int. Genet. 2016;23: 178-189.

de la Puente M, Santos C, Fondevila M, Manzo L; EUROFORGEN-NoE Consortium., Carracedo Á, Lareu MV, Phillips C. The Global AIMs Nano set: a 31-plex SNaPshot assay of ancestry-informative SNPs. Forensic Sci. Int. Genet. 2016;22: 81-88.

Silvia AL, Shugarts N, Smith J. A preliminary assessment of the ForenSeqTMFGx System: next generation sequencing of an STR and SNP multiplex. Int. J. Legal Med. 2017;131(1): 73-86.

The Snipper app suite tool: http:// mathgene.usc.es/Snipper/ Cross validation: http://mathgene.usc.es/Snipper/analysispopfile2_new.html, custom ancestry classifications.

Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb. Investig. Genet. 2012;3(1): 18.

Bulbul O, Cherni L, Khodjet-El-Khil H, Rajeevan H, Kidd KK. Evaluating a subset of ancestry informative SNPs for discriminating among Southwest Asian and circum-Mediterranean populations. Forensic Sci. Int. Genet. 2016;23: 153-158.

Prestes P, John Mitchell R, Runa D, Sánchez J, A.H.van Oorschot R. Predicting biogeographical ancestry in admixed individuals – values and limitations of using uniparental and autosomal markers. Aust. J. Forensic Sci. 2016;48(1): 10-23.

Pereira L, Richards M, Goios A, Alonso A, Albarrán C, Garcia O, et al. Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale. Forensic Sci. Int. 2006;159: 43–50.

Rodriguez-Palau E, Hernandez-Romero A, Salamanca-Rodriguez L, Ruiz-García F, Sardi-Perea E. Colombia. Una Nación Multicultural. Dirección de Censos y Demografía. DANE, Departamento Administrativo Nacional de Estadística, Bogotá. http:// http://www.dane.gov.co.

Yunis JJ, Yunis EJ. Mitochondrial DNA (mtDNA) haplogroups in 1526 unrelated individuals from 11 Departments of Colombia. Genet. Mol. Biol. 2013;36(3):329-335

Xavier C., Builes JJ, Gomes V, Ospino JM, Aquino J, Parson W, Amorim A, Gusmao L, Goios A. Admixture and genetic diversity distribution patterns of non-recombining lineages of native american ancestry in colombian populations. PLoS One 2015;10(3):e0120155.

Chaitanya L, van Oven M, Weiler N, Harteveld J, Wirken L, Sijen T, et al. Developmental validation of mitochondrial DNA genotyping assays for adepts matrilineal inference of biogeographic ancestry at a continental level. Forensic Sci. Int. Genet. 2014;11: 39-51.

Brandstätter A, Parsons T, Parsons W. Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int. J. Legal Med. 2003;117: 291-298.

Kohnemann S, Sibbing U, Pfeiffer H, Hohoff C. A rapid mtDNA assay of 22 SNPs in one multiplex reaction increases the power of forensic testing in European Caucasians. Int. J. Legal Med. 2008;122: 517-523.

Paneto GG, Koehnemann S, Martins JA, Cicarelli RM, Pfeiffer H. A single multiplex PCR and SNaPshot minisequencing reaction of 42 SNPs to clssify admixture populations into mitochondrial DNA haplogroups. Mitochondrion 2011;11: 296-302.

Coutinho A, Valverde G, Fehren-Schmitz L, Cooper A, Barreto Romero MI, Espinoza IF, Llamas B, Haak W. AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas. PLoS One 2014;9(3): e93292.

Diaz-Lacava A, Walier M, Willuweit S, Wienker T, Fimmers R, Baur M, et al. Geostatistical inference of main Y-STR-haplotype groups in Europe. Forensic Sci. Int. Genet. 2011;5: 91-94.

Lao O, Lu T, Nothnagel M, Junge O, Freitag-Wolf S, Caliebe A, et al. Correlation between Genetic and Geographic Structure in Europe. Curr. Biol. 2008;18(16): 1241-1248.

Purps J, Sigert S, Willuweit S, Nagy M, Alves C, Salazar R, et al. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci. Int. Genet. 2014;12: 12-23.

Van Oven M, Ralf A, Kayser M. An efficient multiplex genotyping approach for detecting the major worlwide human Y-chromosome haplogroups. Int. J. Legal Med. 2011;125: 879-885.

Onofri V, Alessandrini F, Turchi C, Pesaresi M, Buscemi L, Tagliabracci A. Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs. Forensic Sci. Int. 2006;157: 23-35.

Geppert M, Baeta M, Núñez C, Martínez-Jarreta B, Zweynert S, Cruz OW, González-Andrade F, González-Solorzano J, Nagy M, Roewer L. Hierarchical Y-SNP assay to study the hidden diversity and phylogenetic relationship of native populations in South America. Forensic Sci. Int. Genet 2011;5(2): 100-104.

Ralf A, van oven M, Zhong K, Kayser M. Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing. Hum. Mutat. 2015;36(1): 151-159.

Phillips C, Fernández-Formoso L, Garcia-Magariños M, Porras L, Tyedebrink T, Amigo J, et al. Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diverity panel. Forensic Sci. Int. Genet. 2011;5: 155-169.

Phillips C, Freire-Aradas A, Kriegel A, Fondevila M, Bulbul O, Santos C, et al. Eurasiaplex: A forensic SNP assay for differentiating European and South Asian ancestries. Forensic Sci. Int. Genet. 2013;7: 359-366.

Phillips C, Prieto L, Fondevila M, Salas A, Gómez-Tato A, Álvarez-Dios J, et al. Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS ONE. 2009;4(8): e6583.

Spector SA, Brummel SS, Nievergelt CM, Maihofer AX, Singh KK, Purswani MU, Williams PL, Hazra R, Van Dyke R, Seage GR 3rd; Pediatric HIVAIDS Cohort Study (PHACS). Genetically determined ancestry is more informative than self-reported race in HIV-infected and -exposed children. Medicine (Baltimore). 2016;95(36): e4733.

Oliveira JS, Ferreira RS, Santos LM, Marin LJ, Corrêa RX, Luizon MR, Simões AL, Gadelha SR, Sousa SM. Self-declared ethnicity and genomic ancestry in prostate cancer patients from Brazil. Genet. Mol. Res. 2016;15(4).

Ley 10/2007, de 8 de octubre, reguladora de la base de datos policial sobre identificadores obtenidos a partir del ADN. Boletín Oficial del Estado, 9 de octubre de 2007, núm. 242, p. 40969-40972.

Zieger M, Utz S. About DNA databasing and investigative genetic analysis of externally visible characteristics: A public survey. Forensic Sci. Int. Genet. 2015;17: 163-172.

How to Cite

1.
Popa DM, Arroyo Pardo E, López Parra AM. Review of biogeographical ancestry markers and their application to forensic investigation. Antistio Rev. Cient. INMLCF Colomb. [Internet]. 2017 Apr. 10 [cited 2025 Dec. 6];4(1). Available from: https://revistasforensesmedicinalegalgovco.biteca.online/index.php/an/article/view/1958

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Published

2017-04-10