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

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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.

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Acknowledgments

IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by FCT, the Portuguese Foundation for Science and Technology. CRACS-INESC Porto is supported by Programa Operacional Ciência, Tecnologia e Inovação (POCTI) e Quadro Comunitário de Apoio III. NJ and DH were supported by grant 196-1962766-2751. LZh received grants from the Russian Academy of Science for Mol & Cell Biol and FSM.

Author information

Authors and Affiliations

  1. Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), R. Dr. Roberto Frias s/n, 4200-465, Porto, Portugal

    Luísa Pereira

  2. Faculdade de Medicina da Universidade do Porto, Porto, Portugal

    Luísa Pereira

  3. General Department of Forensic Sciences & Criminology, Dubai Police GHQ, Dubai, UAE

    Farida Alshamali

  4. Faculty of Health Sciences, Oslo University College, Oslo, Norway

    Rune Andreassen

  5. Department of Biological Sciences, California State University, Sacramento, CA, USA

    Ruth Ballard

  6. Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand

    Wasun Chantratita

  7. Department of Forensic Medicine, Central District Office, National Institute of Scientific Investigation, Daejeon, Republic of Korea

    Nam Soo Cho

  8. Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), CNRS and University Toulouse III Paul Sabatier, Toulouse, France

    Clotilde Coudray & Jean-Michel Dugoujon

  9. Departamento de Ciencias Forenses, Organismo de Investigación Judicial, Poder Judicial, Unidad de Genética Forense, San José, Costa Rica

    Marta Espinoza

  10. Department of Medicine, Metropolitan Hospital, Quito, Ecuador

    Fabricio González-Andrade

  11. School of Forensic & Investigative Sciences, University of Central Lancashire, Preston, UK

    Sibte Hadi

  12. Institute of Legal Medicine, Martin-Luther-University Halle, Halle, Germany

    Uta-Dorothee Immel

  13. Carcinogenesis, Biomarkers and Epidemiology Program, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA

    Catalin Marian

  14. Department Zoology and Physical Anthropology, Faculty of Biology, University Complutense of Madrid, Madrid, Spain

    Antonio Gonzalez-Martin

  15. Forensic DNA Laboratory, Antwerp University Hospital, Edegem, Belgium

    Gerhard Mertens

  16. Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria

    Walther Parson

  17. Núcleo de Ações e Pesquisa em Apoio Diagnóstico, Faculdade de Medicina, Universidade Federal de Minas Gerais (NUPAD/FM-UFMG), Belo Horizonte, Minas Gerais, Brazil

    Carlos Perone

  18. DNA Laboratory, Comisaría general de Policía Científica, University Institute of Research Police Sciences (IUICP), Madrid, Spain

    Lourdes Prieto

  19. Department of Legal Medicine, Shimane University School of Medicine, Izumo, Shimane, Japan

    Haruo Takeshita

  20. Instituto de Investigación en Genética Molecular, Centro Universitario de la Cienega (CUCI-UdeG), Universidad de Guadalajara, Ocotlán, Jalisco, México

    Héctor Rangel Villalobos

  21. Department of Legal Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China

    Zhaoshu Zeng

  22. Institute of General Genetics, The Russian Academy of Sciences, Moscow, Russia

    Lev Zhivotovsky

  23. Laboratory of Artificial Intelligence and Decision Support (LIAAD-INESC), Porto, Portugal

    Rui Camacho

  24. DEI, Faculdade de Engenharia da Universidade do Porto, Porto, Portugal

    Rui Camacho

  25. CRACS-INESC Porto LA, Porto, Portugal

    Nuno A. Fonseca

Authors
  1. Luísa Pereira
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  2. Farida Alshamali
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  3. Rune Andreassen
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  4. Ruth Ballard
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  5. Wasun Chantratita
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  7. Clotilde Coudray
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  8. Jean-Michel Dugoujon
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  12. Uta-Dorothee Immel
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  13. Catalin Marian
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  14. Antonio Gonzalez-Martin
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  15. Gerhard Mertens
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  17. Carlos Perone
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  19. Haruo Takeshita
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  20. Héctor Rangel Villalobos
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  21. Zhaoshu Zeng
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  22. Lev Zhivotovsky
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  23. Rui Camacho
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  24. Nuno A. Fonseca
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Corresponding author

Correspondence to Luísa Pereira.

Additional information

LP delineated the project and collected the database. RC and NAF performed the machine learning analyses, interpreted results and constructed the online calculator. The remaining authors contributed genotype profiles for the database and collaborated in the improvement of the manuscript and of the online tool’s output.

Luísa Pereira and Nuno A. Fonseca contributed equally to this work.

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Pereira, L., Alshamali, F., Andreassen, R. et al. PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile. Int J Legal Med 125, 629–636 (2011). https://doi.org/10.1007/s00414-010-0472-2

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  • DOI: https://doi.org/10.1007/s00414-010-0472-2

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