Skip to main content

Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case

Abstract

In the absence of any other conclusive forensic evidence, DNA profiling is the method of choice for body identification. This study focuses on the case of a carbonized corpse whose complete autosomal short tandem repeat (STR) profile could not lead to direct identification by the investigators. To assist in the progress of investigation, we endeavoured to determine the biogeographical origin and eye colour of the deceased individual. Along with Y chromosome and mitochondrial DNA analyses, we applied a next-generation sequencing (NGS) approach to the study of ancestry informative markers (AIMs) using the HID-Ion AmpliSeq™ Ancestry Panel launched by Thermo Fisher Scientific. This work gave us the opportunity to test this new technology in a real forensic case. Although this study highlights the benefits of such a combined approach, as it markedly improves the specificity of the biogeographical profile, it also underlines the need for the accurate characterization of a larger collection of reference populations and the necessity of caution in data interpretation.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2

References

  1. 1.

    Phillips C, Freire Aradas A, Kriegel AK, Fondevila M, Bulbul O, Santos C, Serrulla Rech F, Perez Carceles MD, Carracedo A, Schneider PM et al (2013) Eurasiaplex: a forensic SNP assay for differentiating European and South Asian ancestries. Forensic Sci Int Genet 7(3):359–366

    CAS  Article  PubMed  Google Scholar 

  2. 2.

    Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, Eduardoff M, Borsting C, Johansen P, Fondevila M et al (2014) Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set. Forensic Sci Int Genet 11:13–25

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Kosoy R, Nassir R, Tian C, White PA, Butler LM, Silva G, Kittles R, Alarcon-Riquelme ME, Gregersen PK, Belmont JW et al (2009) Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat 30(1):69–78

    Article  PubMed  PubMed Central  Google Scholar 

  4. 4.

    Phillips C, Salas A, Sanchez JJ, Fondevila M, Gomez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV et al (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1(3-4):273–280

    CAS  Article  PubMed  Google Scholar 

  5. 5.

    Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, Maiers M, Middha M, Friedlaender FR, Kidd JR (2014) Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet 10:23–32

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    Kayser M (2015) Forensic DNA phenotyping: predicting human appearance from crime scene material for investigative purposes. Forensic Sci Int Genet 18:33–48

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    King TE, Fortes GG, Balaresque P, Thomas MG, Balding D, Maisano Delser P, Neumann R, Parson W, Knapp M, Walsh S et al (2014) Identification of the remains of King Richard III. Nat Commun 5:5631

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Bouakaze C, Keyser C, Crubezy E, Montagnon D, Ludes B (2009) Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis. Int J Leg Med 123(4):315–325

    Article  Google Scholar 

  9. 9.

    Pereira R, Phillips C, Pinto N, Santos C, dos Santos SE, Amorim A, Carracedo A, Gusmao L (2012) Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLoS One 7(1):e29684

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 10.

    Walsh S, Liu F, Ballantyne KN, van Oven M, Lao O, Kayser M (2011) IrisPlex: a sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Forensic Sci Int Genet 5(3):170–180

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Hollard C, Keyser C, Giscard PH, Tsagaan T, Bayarkhuu N, Bemmann J, Crubezy E, Ludes B (2014) Strong genetic admixture in the Altai at the Middle Bronze Age revealed by uniparental and ancestry informative markers. Forensic Sci Int Genet 12:199–207

    CAS  Article  PubMed  Google Scholar 

  12. 12.

    Mendisco F, Keyser C, Hollard C, Seldes V, Nielsen AE, Crubezy E, Ludes B (2011) Application of the iPLEX Gold SNP genotyping method for the analysis of Amerindian ancient DNA samples: benefits for ancient population studies. Electrophoresis 32(3-4):386–393

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Carnese FR, Mendisco F, Keyser C, Dejean CB, Dugoujon JM, Bravi CM, Ludes B, Crubezy E (2010) Paleogenetical study of pre-Columbian samples from Pampa Grande (Salta, Argentina). Am J Phys Anthropol 141(3):452–462

    Article  PubMed  Google Scholar 

  14. 14.

    Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23(2):147

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. 16.

    Fadhlaoui-Zid K, Chennakrishnaiah S, Zemni R, Grinberg S, Herrera RJ, Benammar-Elgaaied A (2012) Sousse, Tunisia: tumultuous history and high Y-STR diversity. Electrophoresis 33(23):3555–3563

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Athey W (2005) Haplogroup prediction from Y-STR values using an allele-frequency approach. J Genet Geneol 1:1–7

    Google Scholar 

  18. 18.

    Eduardoff M, Santos C, de la Puente M, Gross TE, Fondevila M, Strobl C, Sobrino B, Ballard D, Schneider PM, Carracedo A et al (2015) Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM. Forensic Sci Int Genet 17:110–121

    CAS  Article  PubMed  Google Scholar 

  19. 19.

    Daniel R, Santos C, Phillips C, Fondevila M, van Oorschot RA, Carracedo A, Lareu MV, McNevin D (2015) A SNaPshot of next generation sequencing for forensic SNP analysis. Forensic Sci Int Genet 14:50–60

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Borsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N (2014) Evaluation of the Ion Torrent HID SNP 169-plex: A SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 12:144–154

    Article  PubMed  Google Scholar 

  21. 21.

    Seo SB, King JL, Warshauer DH, Davis CP, Ge J, Budowle B (2013) Single nucleotide polymorphism typing with massively parallel sequencing for human identification. Int J Leg Med 127(6):1079–1086

    Article  Google Scholar 

  22. 22.

    Churchill JD, Schmedes SE, King JL, Budowle B (2015) Evaluation of the Illumina Beta Version ForenSeq DNA Signature Prep Kit for use in genetic profiling. Forensic Sci Int Genet 20:20–29

    Article  PubMed  Google Scholar 

  23. 23.

    Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK (2012) Introducing the forensic research/reference on genetics knowledge base, FROG-kb. Investigative Genet 3(1):18

    Article  Google Scholar 

  24. 24.

    Rajeevan H, Soundararajan U, Kidd JR, Pakstis AJ, Kidd KK (2012) ALFRED: an allele frequency resource for research and teaching. Nucleic Acids Res 40(Database issue):D1010–D1015

    CAS  Article  PubMed  Google Scholar 

  25. 25.

    Pakstis AJ, Haigh E, Cherni L, ElGaaied AB, Barton A, Evsanaa B, Togtokh A, Brissenden J, Roscoe J, Bulbul O et al (2015) 52 additional reference population samples for the 55 AISNP panel. Forensic Sci Int Genet 19:269–271

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Gettings KB, Kiesler KM, Vallone PM (2015) Performance of a next generation sequencing SNP assay on degraded DNA. Forensic Sci Int Genet 19:1–9

    CAS  Article  PubMed  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to C. Hollard.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 658 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Hollard, C., Keyser, C., Delabarde, T. et al. Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case. Int J Legal Med 131, 351–358 (2017). https://doi.org/10.1007/s00414-016-1425-1

Download citation

Keywords

  • Next-generation sequencing
  • Ancestry
  • Degraded DNA
  • Unidentified body