International Journal of Legal Medicine

, Volume 125, Issue 5, pp 629–636

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile

  • Luísa Pereira
  • Farida Alshamali
  • Rune Andreassen
  • Ruth Ballard
  • Wasun Chantratita
  • Nam Soo Cho
  • Clotilde Coudray
  • Jean-Michel Dugoujon
  • Marta Espinoza
  • Fabricio González-Andrade
  • Sibte Hadi
  • Uta-Dorothee Immel
  • Catalin Marian
  • Antonio Gonzalez-Martin
  • Gerhard Mertens
  • Walther Parson
  • Carlos Perone
  • Lourdes Prieto
  • Haruo Takeshita
  • Héctor Rangel Villalobos
  • Zhaoshu Zeng
  • Lev Zhivotovsky
  • Rui Camacho
  • Nuno A. Fonseca
Original Article

Abstract

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15–17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator (http://cracs.fc.up.pt/popaffiliator) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Keywords

Online calculator Genotype profile Autosomal STRs Individual affiliation 

References

  1. 1.
    Alves C, Amorim A, Gusmão L, Pereira L (2001) VWA STR genotyping: further inconsistencies between Perkin-Elmer and Promega kits. Int J Leg Med 115:97–99CrossRefGoogle Scholar
  2. 2.
    Pamplona JP, Freitas F, Pereira L (2008) A worldwide database of autosomal markers used by the forensic community. Forensic Sci Int: Genetics Supplement Series 1:656–657CrossRefGoogle Scholar
  3. 3.
    Salas A, Bandelt HJ, Macaulay V, Richards MB (2007) Phylogeographic investigations: the role of trees in forensic genetics. Forensic Sci Int 168:1–13PubMedCrossRefGoogle Scholar
  4. 4.
    Jobling MA (2001) Y-chromosomal SNP haplotype diversity in forensic analysis. Forensic Sci Int 118:158–162PubMedCrossRefGoogle Scholar
  5. 5.
    Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedo A, SNPforID Consortium (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1:273–280PubMedCrossRefGoogle Scholar
  6. 6.
    Phillips C, Prieto L, Fondevila M, Salas A, Gómez-Tato A, Alvarez-Dios J, Alonso A, Blanco-Verea A, Brión M, Montesino M, Carracedo A, Lareu MV (2009) Ancestry analysis in the 11-M Madrid bomb attack investigation. PLoS ONE 4:e6583PubMedCrossRefGoogle Scholar
  7. 7.
    Sanchez JJ, Børsting C, Balogh K, Berger B, Bogus M, Butler JM, Carracedo A, Court DS, Dixon LA, Filipović B, Fondevila M, Gill P, Harrison CD, Hohoff C, Huel R, Ludes B, Parson W, Parsons TJ, Petkovski E, Phillips C, Schmitter H, Schneider PM, Vallone PM, Morling N (2008) Forensic typing of autosomal SNPs with a 29 SNP-multiplex-results of a collaborative EDNAP exercise. Forensic Sci Int Genet 2:176–183PubMedCrossRefGoogle Scholar
  8. 8.
    Allocco DJ, Song Q, Gibbons GH, Ramoni MF, Kohane IS (2007) Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms. BMC Genomics 8:68PubMedCrossRefGoogle Scholar
  9. 9.
    Amorim A, Pereira L (2005) Pros and cons in the use of SNPs in forensic kinship investigation: a comparative analysis with STRs. Forensic Sci Int 150:17–21PubMedCrossRefGoogle Scholar
  10. 10.
    Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298:2381–2385PubMedCrossRefGoogle Scholar
  11. 11.
    Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet 1:e70PubMedCrossRefGoogle Scholar
  12. 12.
    Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB (2003) Human population genetic structure and inference of group membership. Am J Hum Genet 72:578–589PubMedCrossRefGoogle Scholar
  13. 13.
    Evett IW, Pinchin R, Buffery C (1992) An investigation of the feasibility of inferring ethnic origin from DNA profiles. JFSS 32:301–306Google Scholar
  14. 14.
    Meyer E, Wiegand P, Brinkmann B (1995) Phenotype differences of STRs in 7 human populations. Int J Leg Med 107:314–322CrossRefGoogle Scholar
  15. 15.
    Lowe AL, Urquhart A, Foreman LA, Evett IW (2001) Inferring ethnic origin by means of an STR profile. Forensic Sci Int 119:17–22PubMedCrossRefGoogle Scholar
  16. 16.
    Fosella X, Marroni F, Manzoni S, Verzeletti A, De Ferrari F, Cerri N, Presciuttini S (2004) Assigning individuals to ethnic groups based on 13 STR loci. Int Congr Ser 1261:59–61CrossRefGoogle Scholar
  17. 17.
    Graydon M, Cholette F, Ng LK (2009) Inferring ethnicity using 15 autosomal STR loci -comparisons among populations of similar and distinctly different physical traits. Forensic Sci Int Genet 3:251–254PubMedCrossRefGoogle Scholar
  18. 18.
    Klintschar M, Füredi S, Egyed B, Reichenpfader B, Kleiber M (2003) Estimating the ethnic origin (EEO) of individuals using short tandem repeat loci of forensic relevance. Int Congr Ser 1239:53–56CrossRefGoogle Scholar
  19. 19.
    Fridman C, dos Santos PC, Kohler P, Garcia CF, Lopez LF, Massad E, Gattás GJ (2008) Brazilian population profile of 15 STR markers. Forensic Sci Int Genet 2:e1–e4PubMedCrossRefGoogle Scholar
  20. 20.
    Brisighelli F, Capelli C, Boschi I, Garagnani P, Lareu MV, Pascali VL, Carracedo A (2009) Allele frequencies of fifteen STRs in a representative sample of the Italian population. Forensic Sci Int Genet 3:e29–e30PubMedCrossRefGoogle Scholar
  21. 21.
    Herrera-Paz EF, García LF, Aragon-Nieto I, Paredes M (2008) Allele frequencies distributions for 13 autosomal STR loci in 3 Black Carib (Garifuna) populations of the Honduran Caribbean coasts. Forensic Sci Int Genet 3:e5–e10PubMedCrossRefGoogle Scholar
  22. 22.
    Jacewicz R, Jedrzejczyk M, Ludwikowska M, Berent J (2008) Population database on 15 autosomal STR loci in 1000 unrelated individuals from the Lodz region of Poland. Forensic Sci Int Genet 2:e41–e43PubMedCrossRefGoogle Scholar
  23. 23.
    Juárez-Cedillo T, Zuñiga J, Acuña-Alonzo V, Pérez-Hernández N, Rodríguez-Pérez JM, Barquera R, Gallardo GJ, Sánchez-Arenas R, García-Peña Mdel C, Granados J, Vargas-Alarcón G (2008) Genetic admixture and diversity estimations in the Mexican Mestizo population from Mexico City using 15 STR polymorphic markers. Forensic Sci Int Genet 2:e37–e39PubMedCrossRefGoogle Scholar
  24. 24.
    Kraaijenbrink T, Zuniga S, Su B, Shi H, Xiao CJ, Tang WR, de Knijff P (2008) Allele frequency distribution of 21 forensic autosomal STRs in 7 populations from Yunnan, China. Forensic Sci Int Genet 3:e11–e12PubMedCrossRefGoogle Scholar
  25. 25.
    Omran GA, Rutty GN, Jobling MA (2009) Genetic variation of 15 autosomal STR loci in Upper (Southern) Egyptians. Forensic Sci Int Genet 3:e39–e44PubMedCrossRefGoogle Scholar
  26. 26.
    Piatek J, Jacewicz R, Ossowski A, Parafiniuk M, Berent J (2008) Population genetics of 15 autosomal STR loci in the population of Pomorze Zachodnie (NW Poland). Forensic Sci Int Genet 2:e41–e43PubMedCrossRefGoogle Scholar
  27. 27.
    Sánchez-Diz P, Menounos PG, Carracedo A, Skitsa I (2008) 16 STR data of a Greek population. Forensic Sci Int Genet 2:e71–e72PubMedCrossRefGoogle Scholar
  28. 28.
    Sánchez-Diz P, Acosta MA, Fonseca D, Fernández M, Gómez Y, Jay M, Alape J, Lareu MV, Carracedo A, Restrepo CM (2009) Population data on 15 autosomal STRs in a sample from Colombia. Forensic Sci Int Genet 3:e81–e82PubMedCrossRefGoogle Scholar
  29. 29.
    Nie S, Yao J, Yan H, Yang Y, Gu T, Tang W, Li W, Wang B, Xiao C (2008) Genetic data of 15 STR loci in Chinese Yunnan Han population. Forensic Sci Int Genet 3:e1–e3PubMedCrossRefGoogle Scholar
  30. 30.
    Soták M, Petrejcíková E, Bernasovská J, Bernasovský I, Sovicová A, Boronová I, Svicková P, Bôziková A, Gabriková D (2008) Genetic variation analysis of 15 autosomal STR loci in Eastern Slovak Caucasian and Romany (Gypsy) population. Forensic Sci Int Genet 3:e21–e25PubMedCrossRefGoogle Scholar
  31. 31.
    Rubi-Castellanos R, Anaya-Palafox M, Mena-Rojas E, Bautista-España D, Muñoz-Valle JF, Rangel-Villalobos H (2009) Genetic data of 15 autosomal STRs (Identifiler kit) of three Mexican Mestizo population samples from the States of Jalisco (West), Puebla (Center), and Yucatan (Southeast). Forensic Sci Int Genet 3:e71–e76PubMedCrossRefGoogle Scholar
  32. 32.
    Simms TM, Garcia C, Mirabal S, McCartney Q, Herrera RJ (2008) The genetic legacy of the transatlantic slave trade in the island of New Providence. Forensic Sci Int Genet 2:310–317PubMedCrossRefGoogle Scholar
  33. 33.
    Budowle B, Moretti TR (1999) Genotype profiles for six population groups at the 13 CODIS Short Tandem Repeat core loci and other PCRB Based loci. Forensic Sci Commun 1Google Scholar
  34. 34.
    Zhivotovsky LA, Veremeichyk VM, Kuzub NN, Atramentova LA, Udina IG, Kartel NA, Tsybovsky IS (2009) A reference data base on STR allele frequencies in the Belarus population developed from paternity cases. Forensic Sci Int Genet 3:e107–e109PubMedCrossRefGoogle Scholar
  35. 35.
    Zhivotovsky LA, Malyarchuk BA, Derenko MV, Wozniak M, Grzybowski T (2009) Developing STR databases on structured populations: the native South Siberian population versus the Russian population. Forensic Sci Int Genet 3:e111–e116PubMedCrossRefGoogle Scholar
  36. 36.
    Zhivotovsky LA, Akhmetova VL, Fedorova SA, Zhirkova VV, Khusnutdinova EK (2009) An STR database on the Volga-Ural population. Forensic Sci Int Genet 3:e133–e136PubMedCrossRefGoogle Scholar
  37. 37.
    Li C, Li L, Zhao Z, Lin Y, Que T, Liu Y, Xue J (2009) Genetic polymorphism of 17 STR loci for forensic use in Chinese population from Shanghai in East China. Forensic Sci Int Genet 3:e117–e118PubMedCrossRefGoogle Scholar
  38. 38.
    Andreassen R, Pereira L, Dupuy BM, Mevaag B (2009) Icelandic population data for the STR loci in the AMPFlSTR®SGM Plus™ system and the PowerPlex® Y-system. Forensic Sci Int Genet (in press)Google Scholar
  39. 39.
    Tillmar AO, Bäckström G, Montelius K (2009) Genetic variation of 15 autosomal STR loci in a Somali population. Forensic Sci Int Genet 4:e19–e20PubMedCrossRefGoogle Scholar
  40. 40.
    Lopes V, Serra A, Gamero J, Sampaio L, Balsa F, Oliveira C, Batista L, Corte-Real F, Vieira DN, Vide MC, Anjos MJ, Carvalho M (2009) Allelic frequency distribution of 17 STRs from Identifiler and PowerPlex-16 in Central Portugal area and the Azores archipelago. Forensic Sci Int Genet 4:e1–e7PubMedCrossRefGoogle Scholar
  41. 41.
    Witten IH, Frank E (2005) Data Mining: practical machine learning tools and techniques, 2nd Edition, Morgan KaufmannGoogle Scholar
  42. 42.
    Fonseca NA, Camacho R, Pereira L (submitted) On the prediction of an individual affiliation to a major population group based on information from a small set of autosomal STRs—a machine learning approachGoogle Scholar
  43. 43.
    Muro T, Fujihara J, Imamura S, Nakamura H, Yasuda T, Takeshita H (2008) Allele frequencies for 15 STR loci in Ovambo population using AmpFlSTR Identifiler Kit. Leg Med (Tokyo) 10:157–159Google Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Luísa Pereira
    • 1
    • 2
  • Farida Alshamali
    • 3
  • Rune Andreassen
    • 4
  • Ruth Ballard
    • 5
  • Wasun Chantratita
    • 6
  • Nam Soo Cho
    • 7
  • Clotilde Coudray
    • 8
  • Jean-Michel Dugoujon
    • 8
  • Marta Espinoza
    • 9
  • Fabricio González-Andrade
    • 10
  • Sibte Hadi
    • 11
  • Uta-Dorothee Immel
    • 12
  • Catalin Marian
    • 13
  • Antonio Gonzalez-Martin
    • 14
  • Gerhard Mertens
    • 15
  • Walther Parson
    • 16
  • Carlos Perone
    • 17
  • Lourdes Prieto
    • 18
  • Haruo Takeshita
    • 19
  • Héctor Rangel Villalobos
    • 20
  • Zhaoshu Zeng
    • 21
  • Lev Zhivotovsky
    • 22
  • Rui Camacho
    • 23
    • 24
  • Nuno A. Fonseca
    • 25
  1. 1.Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP)PortoPortugal
  2. 2.Faculdade de Medicina da Universidade do PortoPortoPortugal
  3. 3.General Department of Forensic Sciences & CriminologyDubai Police GHQDubaiUAE
  4. 4.Faculty of Health SciencesOslo University CollegeOsloNorway
  5. 5.Department of Biological SciencesCalifornia State UniversitySacramentoUSA
  6. 6.Department of Pathology, Faculty of Medicine, Ramathibodi HospitalMahidol UniversityBangkokThailand
  7. 7.Department of Forensic Medicine, Central District OfficeNational Institute of Scientific InvestigationDaejeonRepublic of Korea
  8. 8.Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse (AMIS)CNRS and University Toulouse III Paul SabatierToulouseFrance
  9. 9.Departamento de Ciencias Forenses, Organismo de Investigación Judicial, Poder JudicialUnidad de Genética ForenseSan JoséCosta Rica
  10. 10.Department of MedicineMetropolitan HospitalQuitoEcuador
  11. 11.School of Forensic & Investigative SciencesUniversity of Central LancashirePrestonUK
  12. 12.Institute of Legal MedicineMartin-Luther-University HalleHalleGermany
  13. 13.Carcinogenesis, Biomarkers and Epidemiology Program, Lombardi Comprehensive Cancer CenterGeorgetown University Medical CenterWashingtonUSA
  14. 14.Department Zoology and Physical Anthropology, Faculty of BiologyUniversity Complutense of MadridMadridSpain
  15. 15.Forensic DNA LaboratoryAntwerp University HospitalEdegemBelgium
  16. 16.Institute of Legal MedicineInnsbruck Medical UniversityInnsbruckAustria
  17. 17.Núcleo de Ações e Pesquisa em Apoio Diagnóstico, Faculdade de MedicinaUniversidade Federal de Minas Gerais (NUPAD/FM-UFMG)Belo HorizonteBrazil
  18. 18.DNA Laboratory, Comisaría general de Policía CientíficaUniversity Institute of Research Police Sciences (IUICP)MadridSpain
  19. 19.Department of Legal MedicineShimane University School of MedicineIzumoJapan
  20. 20.Instituto de Investigación en Genética Molecular, Centro Universitario de la Cienega (CUCI-UdeG)Universidad de GuadalajaraOcotlánMéxico
  21. 21.Department of Legal Medicine, School of Basic Medical SciencesZhengzhou UniversityZhengzhouChina
  22. 22.Institute of General GeneticsThe Russian Academy of SciencesMoscowRussia
  23. 23.Laboratory of Artificial Intelligence and Decision Support (LIAAD-INESC)PortoPortugal
  24. 24.DEIFaculdade de Engenharia da Universidade do PortoPortoPortugal
  25. 25.CRACS-INESC Porto LAPortoPortugal

Personalised recommendations