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Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico)

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Abstract

Background

STR allele frequency databases from populations are necessary to take full advantage of the increased power of discrimination offered by massively parallel sequencing (MPS) platforms.

Material and methods

For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 105 Mestizo (admixed) individuals from Monterrey City (Northeast, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit.

Results

Most of the STR markers were in Hardy Weinberg equilibrium, with a few exceptions. We found 346 different length-based alleles for these 58 STRs; nevertheless, they became 528 alleles when the sequence was assessed. The combined power of discrimination from autosomal STRs (aSTRs) was –virtually– 100% in both length and sequence-based alleles, while the power of exclusion was 99.9999999976065 and 99.9999999999494%, respectively. Haplotypes based on X-STRs and Y-STRs showed 100% of discriminatory capacity.

Conclusions

These results provide –for the first time– forensic genomic population data from Mexico necessary for interpretation in kinship and criminal analyses.

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References

  1. Friis SL, Buchard A, Rockenbauer E, Borsting C, Morling N (2016) Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs. Forensic Sci Int Genet 21:68–75. doi:https://doi.org/10.1016/j.fsigen.2015.12.006

    Article  CAS  PubMed  Google Scholar 

  2. Novroski NM, King JL, Churchill JD, Seah LH, Budowle B (2016) Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Sci Int Genet 25:214–226. doi:https://doi.org/10.1016/j.fsigen.2016.09.007

    Article  CAS  PubMed  Google Scholar 

  3. Casals F, Anglada R, Bonet N, Rasal R, van-der-Gaag KJ, Hoogenboom J, Solé-Morata N, Comas D, Calafell F (2017) Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations. Forensic Sci Int Genet 30:66–70. doi:https://doi.org/10.1016/j.fsigen.2017.06.006

    Article  CAS  PubMed  Google Scholar 

  4. Delest A, Godfrin D, Chantrel Y, Ulus A, Vannier J, Faivre M, Hollard C, Laurent FX (2020) Sequenced-based French population data from 169 unrelated individuals with Verogen´s ForenSeq DNA signature prep kit. Forensic Sci Int Genet 47:102304. doi:https://doi.org/10.1016/j.fsigen.2020.102304

    Article  CAS  PubMed  Google Scholar 

  5. Peng D, Zhang Y, Ren H, Li H, Li R, Shen X, Wang N, Huang E, Wu R, Sun H (2020) Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing. Sci Rep 10(1):12225. doi:https://doi.org/10.1038/s41598-020-69137-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Guevara EK, Palo JU, King JL, Buś MM, Guillén S, Budowle B, Sajantila A (2021) Autosomal STR and SNP characterization of populations from the Northeastern Peruvian Andes with the ForenSeqTM; DNA Signature Prep Kit. Forensic Sci Int Genet 52:102487. doi:https://doi.org/10.1016/j.fsigen.2021.102487

    Article  CAS  PubMed  Google Scholar 

  7. Phillips C, Devesse L, Ballard D, van-Weert L, de-la-Puente M, Melis S, Álvarez-Iglesias V, Freire-Aradas A, Oldroyd N, Holt C, Syndercombe-Court D, Carracedo Á, Lareu MV (2018) Global patterns of STR sequence variation: Sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit. Electrophoresis 39(21):2708–2724. doi:https://doi.org/10.1002/elps.201800117

    Article  CAS  PubMed  Google Scholar 

  8. Barrio PA, Martin P, Alonso A, Muller P, Bodner M, Berger B, Parson W, Budowle B, Consortium D (2019) Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power. Forensic Sci Int Genet 42:49–55

    Article  CAS  Google Scholar 

  9. Just RS, Moreno LI, Smerick JB, Irwin JA (2017) Performance and concordance of the ForenSeq™ system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens. Forensic Sci Int Genet 28:1–9. doi:https://doi.org/10.1016/j.fsigen.2017.01.001

    Article  CAS  PubMed  Google Scholar 

  10. Xu M, Du Q, Ma G, Chen Z, Liu Q, Fu L, Cong B, Li S (2019) Utility of ForenSeq™ DNA Signature Prep Kit in the research of pairwise 2nd-degree kinship identification. Int J Legal Med 33(6):1641–1650. doi:https://doi.org/10.1007/s00414-019-02003-6

    Article  Google Scholar 

  11. Wu J, Li JL, Wang ML, Li JP, Zhao ZC, Wang Q, Yang SD, Xiong X, Yang JL, Deng YJ (2019) Evaluation of the MiSeq FGx system for use in forensic casework. Int J Legal Med 133(3):689–697

    Article  Google Scholar 

  12. Verogene (2020) ForenSeq™ DNA Signature Prep Reference Guide. D2018005 Rev. C. California 92121 U.S.A, San Diego

    Google Scholar 

  13. Parson W, Ballard D, Budowle B, Butler JM, Gettings KB, Gill P, Gusmão L, Hares DR, Irwin JA, King JL, Knijff Pd, Morling N, Prinz M, Schneider PM, Neste CV, Willuweit S, Phillips C (2016) Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements. Forensic Sci Int Genet 22:54–63. doi:https://doi.org/10.1016/j.fsigen.2016.01.009

    Article  CAS  PubMed  Google Scholar 

  14. Verogen (2018) MiSeq FGx™ Instrument Reference Guide. San Diego, CA 92121, U.S.A

  15. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539

    Article  CAS  Google Scholar 

  16. Lewis PO, Zaykin D (2001) GDA (Genetic Data Analysis): Computer Program for the Analysis of Allelic Data. Versión 1.1, University of Connecticut, Storrs. http://phylogeny.uconn.edu/software/

  17. Zaykin DV, Zhivotovsky LA, Westfall PH, Weir BS (2002) Truncated method for combining P-values. Genet Epidemiol 22(2):170–185

    Article  CAS  Google Scholar 

  18. Buckleton J (2005) Validating databases. In: Buckleton J, Triggs CM, Walsh SJ (eds) Forensic DNA evidence interpretation. CRC press, Boca Ration, pp 149–196

    Google Scholar 

  19. Gusmão L, Butler JM, Linacre A, Parson W, Roewer L, Schneider PM, Carracedo A (2017) Revised guidelines for the publication of genetic population data. Forensic Sci Int Genet 30:160–163. doi:https://doi.org/10.1016/j.fsigen.2017.06.007

    Article  CAS  PubMed  Google Scholar 

  20. Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F (2022) A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Sci Int Genet 57:102646. doi: https://doi.org/10.1016/j.fsigen.2021.102646

    Article  CAS  PubMed  Google Scholar 

  21. Ramos-González B, Aguilar-Velázquez JA, Chávez-Briones ML, Delgado-Chavarría JR, Alfaro-Lopez E, Rangel-Villalobos H (2016) Population data of 24 STRs in Mexican-Mestizo population from Monterrey, Nuevo Leon (Northeast, Mexico) based on Powerplex Fusion and GlobalFiler kits. Forensic Sci Int Genet 21:e15–e17. doi:https://doi.org/10.1016/j.fsigen.2015.12.004

    Article  CAS  PubMed  Google Scholar 

  22. Ramos-González B, Aguilar-Velázquez JA, Alfaro-Lopez E, Rangel-Villalobos H (2017) Genetic population data of three Y-STR genetic systems in Mexican-Mestizos from Monterrey, Nuevo León (Northeast, Mexico). Forensic Sci Int Genet 29:e21–e22. https://doi.org/10.1016/j.fsigen.2017.04.016

    Article  CAS  PubMed  Google Scholar 

  23. Bright JA, Allen C, Fountain S, Gray K, Grover D, Neville S, Poyg AL, Taylor D, Turbetti G, Wilson-Wilde L (2014) Australian population data for the twenty Promega PowerPlex 21 short tandem repeat loci. Australian J Forensic Sci 46:442–446

    Article  Google Scholar 

  24. Augustinus D, Gahan ME, McNevin D (2015) Development of a forensic identity SNP panel for Indonesia. Int J Legal Med 129:681–691. doi: https://doi.org/10.1007/s00414-014-1055-4

    Article  PubMed  Google Scholar 

  25. Taylor F, Bright JA, McGovern C, Neville S, Grover D (2017) Allele frequency database for GlobalFiler™ STR loci in Australian and New Zealand populations. Forensic Sci Int Genet 28:e38–e40. doi: https://doi.org/10.1016/j.fsigen.2017.02.012

    Article  CAS  PubMed  Google Scholar 

  26. Kling D, Dell’Amico B, Tillmar AO (2015) FamLinkX - implementation of a general model for likelihood computations for X-chromosomal marker data. Forensic Sci Int Genet 17:1–7. https://doi.org/10.1016/jfsigen201502007

    Article  CAS  PubMed  Google Scholar 

  27. Aguilar-Velázquez JA, Martínez-Cortés G, Inclán-Sánchez A, Favela-Mendoza AF, Velarde-Félix JS, Rangel-Villalobos H (2018) Forensic parameters and admixture in Mestizos from five geographic regions of Mexico based on 20 autosomal STRs (Powerplex 21 system). Int J Legal Med 132(5):1293–1296. doi: https://doi.org/10.1007/s00414-018-1810-z

    Article  PubMed  Google Scholar 

  28. National Research Council (NRCII) Committee on DNA Forensic Science (1996) The Evaluation of Forensic DNA Evidence. National Academy Press, Washington, DC

    Google Scholar 

  29. Balding DJ, Nichols RA (1994) DNA profile match probability calculation: how to allow for population stratification, relatedness, database selection and single bands. Forensic Sci Int 64:125e140

    Article  Google Scholar 

  30. González-Herrera LJ, García-Aceves ME, Domínguez-Cruz MD, López-González PN, Sosa-Escalante JE, Rangel-Villalobos H (2020) A four-step mutation at D22S1045 in one complex paternity case when the brother of the alleged father hypothesis is evaluated. Int J Legal Med 134:1653. doi: https://doi.org/10.1007/s00414-020-02335-8

    Article  PubMed  Google Scholar 

  31. United Nation Human Rights (2021) Conferencia de prensa tras la visita del Comité de la ONU contra la Desaparición Forzada a México. 1–6. https://hchr.org.mx/comunicados/conferencia-de-prensa-tras-la-visita-del-comite-de-la-onu-contra-la-desaparicion-forzada-a-mexico/

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Funding

This project was supported by the Mexican government through CONACyT Ciencia Básica 2016 to H-R-V (Grant 286623).

Author information

Author notes

  1. José Alonso Aguilar-Velázquez and Miguel Ángel Duran-Salazar have contributed equally to this work.

Authors and Affiliations

  1. Instituto de Investigación en Genética Molecular, Centro Universitario de la Ciénega, Universidad de Guadalajara, Av. Universidad #1115, CP 47810, Ocotlán, Jalisco, Mexico

    José Alonso Aguilar-Velázquez, Miguel Ángel Duran-Salazar, Gabriela Martinez-Cortés & Héctor Rangel-Villalobos

  2. Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico

    José Alonso Aguilar-Velázquez

  3. Programa de Doctorado en Biociencias, Centro Universitario de los Altos, Universidad de uadalajara, Tepatitlán de Morelos, Jalisco, Mexico

    Miguel Ángel Duran-Salazar

  4. Instituto de Criminalística y Servicios Periciales, Fiscalía General de Justicia del Estado de Nuevo León (FGJNL), Monterrey, Nuevo León, Mexico

    Miranda Fabiola Córdoba-Mercado, Carolina Elena Coronado-Avila, Orlando Salas-Salas & Benito Ramos-González

  5. Servei de Genómica, Universitat Pampeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Spain

    Ferrán Casals

  6. Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain

    Ferrán Casals

  7. Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003, Barcelona, Spain

    Francesc Calafell

Authors
  1. José Alonso Aguilar-Velázquez
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  2. Miguel Ángel Duran-Salazar
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  3. Miranda Fabiola Córdoba-Mercado
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  4. Carolina Elena Coronado-Avila
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  5. Orlando Salas-Salas
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  6. Gabriela Martinez-Cortés
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  7. Ferrán Casals
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  8. Francesc Calafell
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  9. Benito Ramos-González
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  10. Héctor Rangel-Villalobos
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Corresponding authors

Correspondence to Benito Ramos-González or Héctor Rangel-Villalobos.

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The authors declare no conflicts of interest.

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All individuals signed a written informed consent agreeing to the ethical guidelines of the Helsinki Declaration. This study was approved by the Local Ethical Research Committee. The anonymity of the participants will be preserved at all times.

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Aguilar-Velázquez, J.A., Duran-Salazar, M.Á., Córdoba-Mercado, M.F. et al. Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico). Mol Biol Rep 49, 7601–7609 (2022). https://doi.org/10.1007/s11033-022-07575-y

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