Inferring Biogeographic Ancestry and Its Use in Forensic Sciences

Authors

  • Özlem Bülbül İstanbul Üniversitesi-Cerrahpaşa, Adli Tıp Enstitüsü, İstanbul , İstanbul Üniversitesi-Cerrahpaşa, Adli Tıp Enstitüsü, İstanbul
  • Gönül Filoğlu İstanbul Üniversitesi-Cerrahpaşa, Adli Tıp Enstitüsü, İstanbul , İstanbul Üniversitesi-Cerrahpaşa, Adli Tıp Enstitüsü, İstanbul

DOI:

https://doi.org/10.17986/blm.2019250174

Keywords:

Biogeographic ancestry, SNP, forensic genetics

Abstract

In forensic applications SNP (Single nucleotide polymorphism) markers are used for identification, determination of phenotypes, lineage and ancestry. Ancestry informative SNP markers (AISNPs), which show differences between populations in different geographic regions, are used for estimating of the biogeographic ancestry. The biogeographical origin of a person and the percentage of genetic lineage taken from each biogeographic region can be determined using AISNP markers. This information may assist forensic investigations of unknown contributors or identification of missing persons and disaster victims. In this review, biogeographic ancestry concept, AISNPs panels used in estimation of the biogeographic ancestry, application methods, statistical methods, and current forensic applications has been discussed.

References

Butler JM, Coble MD, Vallone PM. STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic science, medicine, and pathology. 2007;3(3):200-5. https://doi.org/10.1007/s12024-007-0018-1

Budowle B, van Daal A. Forensically relevant SNP classes. BioTechniques. 2008;44(5):603-8, https://doi.org/10.10.2144/000112806

Butler JM, Budowle B, Gill P, Kidd KK, Phillips C, Schneider PM, et al. Report on ISFG SNP Panel Discussion. Forensic Science International: Genetics Supplement Series. 2008;1(1):471-2. https://doi.org/10.1016/j.fsigss.2007.10.159

Gill P. An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. International journal of legal medicine. 2001;114(4-5):204-10.

Race E, Genetics Working G. The use of racial, ethnic, and ancestral categories in human genetics research. American journal of human genetics. 2005;77(4):519-32. https://doi.org/10.1086/491747

Bonilla C, Shriver MD, Parra EJ, Jones A, Fernandez JR. Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York city. Human genetics. 2004;115(1):57-68. https://doi.org/10.1007/s00439-004-1125-7

Tishkoff SA, Kidd KK. Implications of biogeography of human populations for 'race' and medicine. Nature genetics. 2004;36(11 Suppl):S21-7. https://doi.org/10.1038/ng1438

Butler K, Peck M, Hart J, Schanfield M, Podini D. Molecular “eyewitness”: Forensic prediction of phenotype and ancestry. Forensic Science International: Genetics Supplement Series. 2011;3(1):e498-e9. https://doi.org/10.1016/j.fsigss.2011.09.109

Kayser M. Forensic DNA Phenotyping: Predicting human appearance from crime scene material for investigative purposes. Forensic science international Genetics. 2015;18:33-48. https://doi.org/10.1016/j.fsigen.2015.02.003

Rosenberg NA, Li LM, Ward R, Pritchard JK. Informativeness of genetic markers for inference of ancestry. American journal of human genetics. 2003;73(6):1402-22. https://doi.org/10.1086/380416

Phillips C, Fernandez-Formoso L, Gelabert-Besada M, Garcia-Magarinos 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):1151-62. https://doi.org/10.1002/elps.201200621

Algee-Hewitt BF, Edge MD, Kim J, Li JZ, Rosenberg NA. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers. Current biology : CB. 2016;26(7):935-42. https://doi.org/10.1016/j.cub.2016.01.065

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. Human mutation. 2008;29(5):648-58. https://doi.org/10.1002/humu.20695

Frudakis T, Venkateswarlu K, Thomas MJ, Gaskin Z, Ginjupalli S, Gunturi S, et al. A classifier for the SNP-based inference of ancestry. Journal of forensic sciences. 2003;48(4):771-82.

Phillips C. Forensic genetic analysis of bio-geographical ancestry. Forensic science international Genetics. 2015;18:49-65. https://doi.org/10.1016/j.fsigen.2015.05.012

Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, et al. Skin pigmentation, biogeographical ancestry and admixture mapping. Human genetics. 2003;112(4):387-99. https://doi.org/10.1007/s00439-002-0896-y

Bulbul O, Filoglu G, Altuncul H, Aradas AF, Ruiz Y, Fondevila M, et al. A SNP multiplex for the simultaneous prediction of biogeographic ancestry and pigmentation type. Forensic Science International: Genetics Supplement Series. 2011;3(1):e500-e1. https://doi.org/10.1016/j.fsigss.2011.10.001

Phillips C, Salas A, Sanchez JJ, Fondevila M, Gomez-Tato A, Alvarez-Dios J, et al. Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic science international Genetics. 2007;1(3-4):273-80. https://doi.org/10.1016/j.fsigen.2007.06.008

Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, et al. Progress toward an efficient panel of SNPs for ancestry inference. Forensic science international Genetics. 2014;10:23-32. https://doi.org/10.1016/j.fsigen.2014.01.002

Phillips C, Freire Aradas A, Kriegel AK, Fondevila M, Bulbul O, Santos C, et al. Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries. Forensic science international Genetics. 2013;7(3):359-66. https://doi.org/10.1016/j.fsigen.2013.02.010

Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, et al. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Human mutation. 2009;30(1):69-78. https://doi.org/10.1002/humu.20822

Fondevila M, Phillips C, Santos C, Freire Aradas A, Vallone PM, Butler JM, et al. Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies. Forensic science international Genetics. 2013;7(1):63-74. https://doi.org/10.1016/j.fsigen.2012.06.007

Phillips C, Prieto L, Fondevila M, Salas A, Gomez-Tato A, Alvarez-Dios J, et al. Ancestry analysis in the 11-M Madrid bomb attack investigation. PloS one. 2009;4(8):e6583. https://doi.org/10.1371/journal.pone.0006583

Nassir R, Kosoy R, Tian C, White PA, Butler LM, Silva G, et al. An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels. BMC genetics. 2009;10:39. https://doi.org/10.1186/1471-2156-10-39

Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, et al. Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set. Forensic science international Genetics. 2014;11:13-25. https://doi.org/10.1016/j.fsigen.2014.02.012

Mehta B, Daniel R, Phillips C, Doyle S, Elvidge G, McNevin D. Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq. Electrophoresis. 2016;37(21):2832-40. https://doi.org/10.1002/elps.201600190

Pakstis AJ, Kang L, Liu L, Zhang Z, Jin T, Grigorenko EL, et al. Increasing the reference populations for the 55 AISNP panel: the need and benefits. International journal of legal medicine. 2017;131(4);913-917 https://doi.org/10.1007/s00414-016-1524-z

Pakstis AJ, Haigh E, Cherni L, ElGaaied ABA, Barton A, Evsanaa B, et al. 52 Additional Reference Population Samples for the 55 AISNP panel. Forensic Sci Int Genet. 2015;(19):269-271. https://doi.org/10.1016/j.fsigen.2015.08.003

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 science international Genetics. 2016;23:153-8. https://doi.org/10.1016/j.fsigen.2016.04.010

Bulbul O, Filoglu G, Zorlu T, Altuncul H, Freire-Aradas A, Sochtig J, et al. Inference of biogeographical ancestry across central regions of Eurasia. International journal of legal medicine. 2016;130(1):73-9. https://doi.org/10.1007/s00414-015-1246-7

Bulbul O, Speed WC, Gurkan C, Soundararajan U, Rajeevan H, Pakstis AJ, et al. Improving ancestry distinctions among Southwest Asian populations. Forensic science international Genetics. 2018;35:14-20. https://doi.org/10.1016/j.fsigen.2018.03.010

Gettings KB, Lai R, Johnson JL, Peck MA, Hart JA, Gordish-Dressman H, et al. A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population. Forensic science international Genetics. 2014;8(1):101-8. https://doi.org/10.1016/j.fsigen.2013.07.010

Santos C, Phillips C, Fondevila M, Daniel R, van Oorschot RA, Burchard EG, et al. Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region. Forensic science international Genetics. 2016;20:71-80. https://doi.org/10.1016/j.fsigen.2015.10.003

Daca-Roszak P, Pfeifer A, Zebracka-Gala J, Jarzab B, Witt M, Zietkiewicz E. EurEAs_Gplex--A new SNaPshot assay for continental population discrimination and gender identification. Forensic science international Genetics. 2016;20:89-100. https://doi.org/10.1016/j.fsigen.2015.10.004

Wei YL, Wei L, Zhao L, Sun QF, Jiang L, Zhang T, et al. A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents. International journal of legal medicine. 2016;130(1):27-37. https://doi.org/10.1007/s00414-015-1183-5

de la Puente M, Santos C, Fondevila M, Manzo L, Consortium EU-N, Carracedo A, et al. The Global AIMs Nano set: A 31-plex SNaPshot assay of ancestry-informative SNPs. Forensic science international Genetics. 2016;22:81-8. https://doi.org/10.1016/j.fsigen.2016.01.015

Churchill JD, Schmedes SE, King JL, Budowle B. Evaluation of the Illumina((R)) Beta Version ForenSeq DNA Signature Prep Kit for use in genetic profiling. Forensic science international Genetics. 2016;20:20-9. https://doi.org/10.1016/j.fsigen.2015.09.009

Bulbul O, Filoglu G. Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing. Electrophoresis. 2018;39(21):2743-51. https://doi.org/10.1002/elps.201800243

Li CX, Pakstis AJ, Jiang L, Wei YL, Sun QF, Wu H, et al. A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia. Forensic science international Genetics. 2016;23:101-10. https://doi.org/10.1016/j.fsigen.2016.04.002

Truelsen DM, Farzad MS, Mogensen HS, Pereira V, Tvedebrink T, Børsting C, et al. Typing of two Middle Eastern populations with the Precision ID Ancestry Panel. Forensic Sci Int Genet Suppl Ser. 2017;6:e301-e2. https://doi.org/10.1016/j.fsigss.2017.09.133

Sobrino B, Brion M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int. 2005;154(2-3):181-94. https://doi.org/10.1016/j.forsciint.2004.10.020

Mehta B, Daniel R, Phillips C, McNevin D. Forensically relevant SNaPshot(R) assays for human DNA SNP analysis: a review. International journal of legal medicine. 2017;131(1):21-37. https://doi.org/10.1007/s00414-016-1490-5

Walsh S, Liu F, Wollstein A, Kovatsi L, Ralf A, Kosiniak-Kamysz A, et al. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic science international Genetics. 2013;7(1):98-115. https://doi.org/10.1016/j.fsigen.2012.07.005

Walsh S, Liu F, Ballantyne KN, van Oven M, Lao O, Kayser M. IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic science international Genetics. 2011;5(3):170-80. https://doi.org/10.1016/j.fsigen.2010.02.004

Daniel R, Santos C, Phillips C, Fondevila M, van Oorschot RA, Carracedo A, et al. A SNaPshot of next generation sequencing for forensic SNP analysis. Forensic science international Genetics. 2015;14:50-60. https://doi.org/10.1016/j.fsigen.2014.08.013

Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, et al. Genetic structure of human populations. Science. 2002;298(5602):2381-5. https://doi.org/10.1126/science.1078311

Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. Introducing the Forensic Research/Reference on Genetics knowledge base, FROG-kb. Investigative genetics. 2012;3(1):18. https://doi.org/10.1186/2041-2223-3-18

Kidd KK, Soundararajan U, Rajeevan H, Pakstis AJ, Moore KN, Ropero-Miller JD. The redesigned Forensic Research/Reference on Genetics-knowledge base, FROG-kb. Forensic science international Genetics. 2017;33:33-7. https://doi.org/10.1016/j.fsigen.2017.11.009

Pakstis AJ, Kang L, Liu L, Zhang Z, Jin T, Grigorenko EL, et al. Increasing the reference populations for the 55 AISNP panel: the need and benefits. Int J Legal Med. 2017;131(4):913-7. https://doi.org/10.1007/s00414-016-1524-z

Amigo J, Salas A, Phillips C, Carracedo A. SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC bioinformatics. 2008;9:428. https://doi.org/10.1186/1471-2105-9-428

Kayser M, de Knijff P. Improving human forensics through advances in genetics, genomics and molecular biology. Nature reviews Genetics. 2011;12(3):179-92. https://doi.org/10.1038/nrg2952

Kayser M, Schneider PM. DNA-based prediction of human externally visible characteristics in forensics: motivations, scientific challenges, and ethical considerations. Forensic science international Genetics. 2009;3(3):154-61. https://doi.org/10.1016/j.fsigen.2009.01.012

Downloads

Published

2019-10-13

Issue

Section

Review

How to Cite

1.
Bülbül Özlem, Filoğlu G. Inferring Biogeographic Ancestry and Its Use in Forensic Sciences. Bull Leg Med [Internet]. 2019 Oct. 13 [cited 2025 Dec. 8];24(2):131-40. Available from: https://www.adlitipbulteni.com/index.php/atb/article/view/1251