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Effective resolution of the Y chromosome sublineages of the Iberian haplogroup R1b-DF27 with forensic purposes

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Abstract

Single-nucleotide polymorphisms (SNPs) found within the non-recombining region of the Y chromosome (NRY) represent a powerful tool in forensic genetics for inferring the paternal ancestry of a vestige and complement the determination of biogeographical origin in combination with other markers like AIMs. In the present study, we introduce a panel of 15 Y-SNPs for a fine-resolution subtyping of the haplogroup R1b-DF27, in a single minisequencing reaction. This is the first minisequencing panel that allows a fine subtyping of R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations. This panel includes subhaplogroups of DF27 that display moderate geographical differentiation, of interest to link a sample with a specific location of the Iberian Peninsula or with Iberian ancestry. Conversely, part of the intricacy of a new minisequencing panel is to have all the included variants available to test the effectiveness of the analysis method. We have overcome the absence of the least common variants through site-directed mutagenesis. Overall, the results show that our panel is a robust and effective method for subtyping R1b-DF27 lineages from a minimal amount of DNA, and its high resolution enables to improve male lineage discrimination in Iberian and Southwest European descent individuals. The small length of the amplicons and its reproducibility makes this assay suitable for forensic and population genetics purposes.

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References

  1. Jobling MA, Pandya A, Tyler-Smith C (1997) The Y chromosome in forensic analysis and paternity testing. Int J Legal Med 110:118–124

    Article  CAS  PubMed  Google Scholar 

  2. Sobrino B, Brión M, Carracedo A (2005) SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 154:181–194

    Article  CAS  PubMed  Google Scholar 

  3. Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonné-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26:358–361. https://doi.org/10.1038/81685

    Article  CAS  PubMed  Google Scholar 

  4. Kayser M (2017) Forensic use of Y-chromosome DNA: a general overview. Hum Genet 136:621–635. https://doi.org/10.1007/s00439-017-1776-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Myres NM, Rootsi S, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Pshenichnov A, Yunusbayev B, Balanovsky O, Balanovska E, Rudan P, Baldovic M, Herrera RJ, Chiaroni J, di Cristofaro J, Villems R, Kivisild T, Underhill PA (2011) A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. Eur J Hum Genet 19:95–101. https://doi.org/10.1038/ejhg.2010.146

    Article  PubMed  Google Scholar 

  6. Cruciani F, Trombetta B, Antonelli C, Pascone R, Valesini G, Scalzi V, Vona G, Melegh B, Zagradisnik B, Assum G, Efremov GD, Sellitto D, Scozzari R (2011) Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152. Forensic Sci Int Genet 5:e49–e52. https://doi.org/10.1016/j.fsigen.2010.07.006

    Article  CAS  PubMed  Google Scholar 

  7. Busby GBJ, Brisighelli F, Sánchez-Diz P et al (2012) The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proc Biol Sci 279:884–892. https://doi.org/10.1098/rspb.2011.1044

    Article  PubMed  Google Scholar 

  8. Valverde L, Illescas MJ, Villaescusa P, Gotor AM, García A, Cardoso S, Algorta J, Catarino S, Rouault K, Férec C, Hardiman O, Zarrabeitia M, Jiménez S, Pinheiro MF, Jarreta BM, Olofsson J, Morling N, de Pancorbo MM (2016) New clues to the evolutionary history of the main European paternal lineage M269: dissection of the Y-SNP S116 in Atlantic Europe and Iberia. Eur J Hum Genet 24:437–441. https://doi.org/10.1038/ejhg.2015.114

    Article  PubMed  Google Scholar 

  9. Rocca RA, Magoon G, Reynolds DF, Krahn T, Tilroe VO, Op den Velde Boots PM, Grierson AJ (2012) Discovery of Western European R1b1a2 Y chromosome variants in 1000 genomes project data: an online community approach. PLoS One 7:e41634. https://doi.org/10.1371/journal.pone.0041634

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Villaescusa P, Illescas MJ, Valverde L, Baeta M, Nuñez C, Martínez-Jarreta B, Zarrabeitia MT, Calafell F, de Pancorbo MM (2017) Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain. Forensic Sci Int Genet 27:142–148. https://doi.org/10.1016/j.fsigen.2016.12.013

    Article  CAS  PubMed  Google Scholar 

  11. Solé-Morata N, Villaescusa P, García-Fernández C, Font-Porterias N, Illescas MJ, Valverde L, Tassi F, Ghirotto S, Férec C, Rouault K, Jiménez-Moreno S, Martínez-Jarreta B, Pinheiro MF, Zarrabeitia MT, Carracedo Á, de Pancorbo MM, Calafell F (2017) Analysis of the R1b-DF27 haplogroup shows that a large fraction of Iberian Y-chromosome lineages originated recently in situ. Sci Rep 7:7341. https://doi.org/10.1038/s41598-017-07710-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Mehta B, Daniel R, Phillips C, McNevin D (2017) Forensically relevant SNaPshot® assays for human DNA SNP analysis: a review. Int J Legal Med 131:21–37. https://doi.org/10.1007/s00414-016-1490-5

    Article  PubMed  Google Scholar 

  13. Palencia-Madrid L, Cardoso S, Castro-Maestre F, Baroja-Careaga I, Rocandio AM, de Pancorbo MM (2018) Development of a new screening method to determine the main 52 mitochondrial haplogroups through a single minisequencing reaction. Mitochondrion S1567-7249:30312–30314. https://doi.org/10.1016/j.mito.2018.02.004

    Article  CAS  Google Scholar 

  14. Van Oven M, Van Geystelen A, Kayser M et al (2014) Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. Hum Mutat 35:187–191. https://doi.org/10.1002/humu.22468

    Article  CAS  PubMed  Google Scholar 

  15. International Society of Genetic Genealogy (2016). Y-DNA haplogroup tree 2016, Version 10.01. http://isogg.org/tree/. Accessed 1 Sep 2017

  16. Marshall OJ (2004) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 20:2471–2472. https://doi.org/10.1093/bioinformatics/bth254

    Article  CAS  Google Scholar 

  17. Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37:226–231

    Article  CAS  Google Scholar 

  18. Sanchez JJ, Børsting C, Morling N (2005) Typing of Y chromosome SNPs with multiplex PCR methods. Methods Mol Biol 297:209–228

    CAS  PubMed  Google Scholar 

  19. 1000 Genomes Project Consortium, Auton A, Brooks LD et al (2015) A global reference for human genetic variation. Nature 526:68–74. https://doi.org/10.1038/nature15393

    Article  CAS  Google Scholar 

  20. Larmuseau MHD, Calafell F, Princen SA, Decorte R, Soen V (2018) The black legend on the Spanish presence in the low countries: verifying shared beliefs on genetic ancestry. Am J Phys Anthropol 166:219–227. https://doi.org/10.1002/ajpa.23409

    Article  PubMed  Google Scholar 

  21. Sauer CO (2008) The early Spanish main. Cambridge University Press

  22. Noguera MC, Schwegler A, Gomes V, Briceño I, Alvarez L, Uricoechea D, Amorim A, Benavides E, Silvera C, Charris M, Bernal JE, Gusmão L (2013) Colombia’s racial crucible: Y chromosome evidence from six admixed communities in the Department of Bolivar. Ann Hum Biol 41:453–459. https://doi.org/10.3109/03014460.2013.852244

    Article  PubMed  Google Scholar 

  23. Morales Padron F (1990) Historia del Decubrimiento y Conquista de América. Gredos

  24. Onofri V, Alessandrini F, Turchi C, Pesaresi M, Buscemi L, Tagliabracci A (2006) Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs. Forensic Sci Int 157:23–35. https://doi.org/10.1016/j.forsciint.2005.03.014

    Article  CAS  PubMed  Google Scholar 

  25. Valverde L, Köhnemann S, Cardoso S, Pfeiffer H, de Pancorbo MM (2013) Improving the analysis of Y-SNP haplogroups by a single highly informative 16 SNP multiplex PCR-minisequencing assay. Electrophoresis 34:605–612. https://doi.org/10.1002/elps.201200433

    Article  CAS  PubMed  Google Scholar 

  26. Bouakaze C, Keyser C, Amory S, Crubézy E, Ludes B (2007) First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA. Int J Legal Med 121:493–499. https://doi.org/10.1007/s00414-007-0177-3

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

The authors are grateful to PhD Maite Álvarez for her human and technical assistance provided on the DNA Bank Service (SGIker) of the University of the Basque Country UPV/EHU (European funding: ERDF and ESF), as well as to the Basque Foundation of Science (BIOEF), and to all the people who voluntarily participated in this study.

Funding

Funds were provided by the Basque Government (IT-424-07 and IT-833-13). During the execution of this study, Patricia Villaescusa was granted with a predoctoral fellowship by the University of the Basque Country UPV/EHU and Leire Palencia-Madrid with a postdoctoral fellowship by the University of the Basque Country UPV/EHU.

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Author notes

  1. Patricia Villaescusa and Leire Palencia-Madrid contributed equally to this work.

Authors and Affiliations

  1. BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Avda. Miguel de Unamuno, 3, 01006, Vitoria-Gasteiz, Spain

    Patricia Villaescusa, Leire Palencia-Madrid, Magdalena Antònia Campaner, Jaione Jauregui-Rada, Miguel Guerra-Rodríguez, Ana María Rocandio & Marian M. de Pancorbo

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  1. Patricia Villaescusa
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  2. Leire Palencia-Madrid
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  3. Magdalena Antònia Campaner
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  4. Jaione Jauregui-Rada
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  5. Miguel Guerra-Rodríguez
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  6. Ana María Rocandio
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  7. Marian M. de Pancorbo
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Corresponding author

Correspondence to Marian M. de Pancorbo.

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Electronic supplementary material

Supplementary Fig. S1

Phylogenetic tree of the Y-SNPs included in the 15-plex minisequencing panel (PNG 18.1 kb)

High resolution image (TIFF 1914 kb)

Supplementary Fig. S2

Electropherogram obtained during the optimization of the 15-plex minisequencing assay, where spurious peaks and pull-ups (circled) can be observed (PNG 11.1 kb)

High resolution image (TIFF 1842 kb)

Supplementary Fig. S3

Diagram of the theoretical positions of the Y-SNPs included in the 15-plex minisequencing panel. Ancestral alleles appear in bold letters; Derived alleles appear underlined (PNG 38.4 kb)

High resolution image (TIFF 1366 kb)

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(XLSX 28.1 kb)

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Villaescusa, P., Palencia-Madrid, L., Campaner, M.A. et al. Effective resolution of the Y chromosome sublineages of the Iberian haplogroup R1b-DF27 with forensic purposes. Int J Legal Med 133, 17–23 (2019). https://doi.org/10.1007/s00414-018-1936-z

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  • DOI: https://doi.org/10.1007/s00414-018-1936-z

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