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Comparison of the genetic background of different Colombian populations using the SNPforID 52plex identification panel

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Abstract

Various strategies for analysing SNP markers and genotyping have been published with the goal of obtaining informative profiles from biological samples that contain only small amounts of template and/or degraded DNA. In this study, a multiplex assay of 52 autosomal single-nucleotide polymorphisms (SNPs) was used to analyse 438 individuals from urban populations from different regions of Colombia, as well as a sample of 50 Native American individuals of the Pastos ethnic group from Nariño. To determine if significant differences in these 52 SNPs exist between the distinct regions of Colombia, genetic distance and admixture analyses were performed based on the available data for 17 different Colombian population groups and for population groups from Africa, Europe and America. The results demonstrate significant differences between the populations from the Southwest Andean, Central-West Andean, Central-East Andean, Orinoquian and northern Colombian Pacific Coast regions. Most of the regions exhibited a European and Native American admixture. One exception is the population from the region of Chocó (on the northern Pacific Coast), which exhibits a high proportion of African admixture (54 %). From the observed genetic backgrounds, it is possible to conclude that a single reference database for the entire country would not be suitable for forensic purposes. The allele frequencies and the forensically relevant parameters were calculated for all of the markers in each Colombian region with significant values for the combined matching probability (power of discrimination ≥0.99999999999999990) and the combined probability of exclusion (≥0.9990) in trios that were obtained from all of the population groups.

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References

  1. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D, The International SNP, Group MW (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928–933. doi:10.1038/35057149

    Article  CAS  PubMed  Google Scholar 

  2. Nachman M (2001) Single nucleotide polymorphisms and recombination rate in humans. Trends Genet 17:481–485. doi:10.1016/S0168-9525(01)02409-X

    Article  CAS  PubMed  Google Scholar 

  3. Fondevila M, Phillips C, Naverán N, Fernández L, Cerezo M, Salas A, Carracedo Á, Lareu MV (2008) Case report: identification of skeletal remains using short-amplicon marker analysis of severely degraded DNA extracted from a decomposed and charred femur. Forensic Sci Int Genet 2:212–218. doi:10.1016/j.fsigen.2008.02.005

    Article  CAS  PubMed  Google Scholar 

  4. Phillips C, Fondevila M, García-Magariños M, Rodríguez A, Salas A, Carracedo Á, Lareu MV (2008) Resolving relationship tests that show ambiguous STR results using autosomal SNPs as supplementary markers. Forensic Sci Int Genet 2:198–204. doi:10.1016/j.fsigen.2008.02.002

    Article  CAS  PubMed  Google Scholar 

  5. Gomes C, Magalhães M, Alves C, Amorim A, Pinto N, Gusmão L (2012) Comparative evaluation of alternative batteries of genetic markers to complement autosomal STRs in kinship investigations: autosomal indels vs. X-chromosome STRs. Int J Legal Med 126:917–921. doi:10.1007/s00414-012-0768-5

    Article  PubMed  Google Scholar 

  6. Pinto N, Magalhães M, Conde-Sousa E, Gomes C, Pereira R, Alves C, Gusmão L, Amorim A (2013) Assessing paternities with inconclusive STR results: the suitability of bi-allelic markers. Forensic Sci Int Genet 7:16–21. doi:10.1016/j.fsigen.2012.05.002

    Article  CAS  PubMed  Google Scholar 

  7. Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27:1713–1724. doi:10.1002/elps.200500671

    Article  CAS  PubMed  Google Scholar 

  8. Pereira R, Fondevila M, Phillips C, Amorim A, Carracedo Á, Gusmão L (2008) Genetic characterization of 52 autosomal SNPs in the Portuguese population. Forensic Sci Int Genet Suppl Ser 1:358–360. doi:10.1016/j.fsigss.2007.10.160

    Article  Google Scholar 

  9. Pereira R, Fondevila M, Phillips C, Amorim A, Carracedo Á, Gusmão L (2008) Genetic characterization of 52 autosomal SNPs in two sub-Saharan African populations. Forensic Sci Int Genet Suppl Ser 1:361–363. doi:10.1016/j.fsigss.2007.10.155

    Article  Google Scholar 

  10. Santos C, Phillips C, Fondevila M, Porras-Hurtado L, Carracedo Á, Souto L, Lareu MV (2011) A study of East Timor variability using the SNPforID 52-plex SNP panel. Forensic Sci Int Genet 5:e25–e26. doi:10.1016/j.fsigen.2010.03.006

    Article  CAS  PubMed  Google Scholar 

  11. Barbaro A, Phillips C, Fondevila M, Lareu MV, Carracedo Á (2012) Genetic variability of the SNPforID 52-plex identification SNP panel in Italian population samples. Forensic Sci Int Genet 6:e185–e186. doi:10.1016/j.fsigen.2012.07.002

    Article  CAS  PubMed  Google Scholar 

  12. Porras L, Phillips C, Fondevila M, Beltran L, Ortiz T, Rondon F, Barreto G, Lareu MV, Henao J, Carracedo Á (2009) Genetic variability of the SNPforID 52-plex identification-SNP panel in Central West Colombia. Forensic Sci Int Genet 4:e9–e10. doi:10.1016/j.fsigen.2008.12.003

    Article  CAS  PubMed  Google Scholar 

  13. O’Rourke DH, Raff JA (2010) The human genetic history of the Americas: the final frontier. Curr Biol 20:R202–R207. doi:10.1016/j.cub.2009.11.051

    Article  PubMed  Google Scholar 

  14. Bravo ML, Moreno MA, Builes JJ, Salas A, Lareu MV, Carracedo A (2001) Autosomal STR genetic variation in negroid Chocó and Bogotá populations. Int J Legal Med 115:102–104. doi:10.1007/s004140100223

    Article  CAS  PubMed  Google Scholar 

  15. Paredes M, Galindo A, Bernal M, Avila S, Andrade D, Vergara C, Rincón M, Romero RE, Navarrete M, Cárdenas M, Ortega J, Suarez D, Cifuentes A, Salas A, Carracedo A (2004) Analysis of the CODIS autosomal STR loci in four main Colombian regions. Erratum in: Forensic Sci Int 143:73–74. doi:10.1016/S0379-0738(03)00271-8

    CAS  Google Scholar 

  16. Yunis JJ, Garcia O, Cuervo AG, Guio E, Pineda CR, Yunis EJ (2005) Population data for PowerPlex 16 in thirteen departments and the capital city of Colombia. J Forensic Sci 50:685–702

    PubMed  Google Scholar 

  17. Builes JJ, Martínez B, Gómez A, Caraballo L, Espinal C, Aguirre D, Montoya A, Moreno M, Amorim A, Gusmão L, Bravo ML (2007) Y chromosome STR haplotypes in the Caribbean city of Cartagena (Colombia). Forensic Sci Int 167:62–69. doi:10.1016/j.forsciint.2005.12.015

    Article  CAS  PubMed  Google Scholar 

  18. Carvajal-Carmona LG, Soto ID, Pineda N, Ortíz-Barrientos D, Duque C, Ospina-Duque J, McCarthy M, Montoya P, Alvarez VM, Bedoya G, Ruiz-Linares A (2000) Strong Amerind/white sex bias and a possible Sephardic contribution among the founders of a population in northwest Colombia. Am J Hum Genet 67:1287–1295. doi:10.1016/S0002-9297(07)62956-5

    CAS  PubMed Central  PubMed  Google Scholar 

  19. Rojas W, Parra MV, Campo O, Caro MA, Lopera JG, Arias W, Duque C, Naranjo A, García J, Vergara C, Lopera J, Hernandez E, Valencia A, Caicedo Y, Cuartas M, Gutiérrez J, López S, Ruiz-Linares A, Bedoya G (2010) Genetic make up and structure of Colombian populations by means of uniparental and biparental DNA markers. Am J Phys Anthropol 143:13–20. doi:10.1002/ajpa.21270

    Article  PubMed  Google Scholar 

  20. Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Walsh PS, Metzger DA, Higuchi R (1991) Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Bio Techniques 10:506–513

    CAS  Google Scholar 

  22. Tereba A (1999) Tools for analysis of population statistics. Profiles in DNA. Promega Corp, Madison

    Google Scholar 

  23. Schneider S, Roessli D, Excoffier L (2011) Arlequin ver 3.5.1.3: a software for population genetics data analysis, genetics and biometry laboratory. University of Geneva, Switzerland

    Google Scholar 

  24. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  Google Scholar 

  25. Cerón Solarte B, Ramos MT (1997) Pasto: espacio, economía y cultura. In: Colección sol de los pastos. Fondo Mixto de Cultura–Nariño, Colombia

    Google Scholar 

  26. Friedemann NS (1993) La saga del negro: presencia africana en Colombia. Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana

  27. Curtin PD (1969) The Atlantic slave trade. A census. The University of Wisconsin Press, Madison

    Google Scholar 

Download references

Acknowledgments

The authors wish to thank Oscar Palacio, Tomas Restrepo, Yeny Posada, Silvana Zapata, Zoraida Florez, Gloria Galeano, Luz Mariela Ochoa and Liliana Porras for their help in sample typing and data revising and analysis. Likewise, the authors would like to thank the Ipiales’ residents, Cuaspud-Carlosama rural community and especially Dr. Martha Castañeda for her support in field sampling logistics. This work was supported by funding from Xunta de Galicia INCITE 09 208163PR (PI: Victoria Lareu). IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Education and Science and is partially supported by FCT. LG is supported by a grant from CAPES, Brazil. AFA was supported by a María Barbeito grant from Xunta de Galicia (Spain). MF is funded by a grant from the postdoctoral programme of the Foundation Barrié de La Maza.

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Authors and Affiliations

  1. IdentiGEN-Genetic Identification Laboratory and Research Group of Genetic Identification, School of Natural and Exact Sciences (FCEN), University of Antioquia, Calle 67, 53-108, Bloque 7-321, Medellin, Colombia

    Adriana Ibarra & Martha Martínez

  2. Institute of Forensic Sciences, Genomic Medicine Group Luis Concheiro, University of Santiago de Compostela, Galicia, Spain

    Ana Freire-Aradas, Manuel Fondevila & Angel Carracedo

  3. Molecular Genetics Laboratory, Cruz Vital. Ecuadorian Red Cross, C11. Papallacta OE1-62 y Av de la Prensa, Quito, Ecuador

    German Burgos

  4. Institute of Legal Medicine and Forensic Sciences, Street 21 No. 22-67 B. La Esperanza, Northeast Regional, Arauca, Colombia

    Mauricio Camacho

  5. Genomic Medicine Laboratory, Health Faculty, Surcolombiana University, Street 9 No. 14-03, Neiva, Huila, Colombia

    Henry Ostos

  6. Clinical Laboratory Olga Zuleima Suárez Molina, Av. 0 No. 11-161 Consultorio 103 Edificio Negomón, Cúcuta, Colombia

    Zuleyma Suarez

  7. Medical and Human Genetics Laboratory, Federal University of Pará (UFPA), Av. Augusto Corrêa, 01, Caixa Postal 8615, 66075-970, Belém, Pará, Brazil

    Sidney Santos & Leonor Gusmão

  8. IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, R. Dr. Roberto Frias s/n, 4200-465, Porto, Portugal

    Leonor Gusmão

Authors
  1. Adriana Ibarra
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  2. Ana Freire-Aradas
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  3. Martha Martínez
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  4. Manuel Fondevila
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  5. German Burgos
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  6. Mauricio Camacho
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  7. Henry Ostos
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  8. Zuleyma Suarez
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  9. Angel Carracedo
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  10. Sidney Santos
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  11. Leonor Gusmão
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Corresponding author

Correspondence to Leonor Gusmão.

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Ibarra, A., Freire-Aradas, A., Martínez, M. et al. Comparison of the genetic background of different Colombian populations using the SNPforID 52plex identification panel. Int J Legal Med 128, 19–25 (2014). https://doi.org/10.1007/s00414-013-0858-z

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  • DOI: https://doi.org/10.1007/s00414-013-0858-z

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