Top

Published in:

01-03-2017 | Case Report

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

Authors: C. Hollard, C. Keyser, T. Delabarde, A. Gonzalez, C. Vilela Lamego, V. Zvénigorosky, B. Ludes

Published in: International Journal of Legal Medicine | Issue 2/2017

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.

Available only for authorised users

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):359–366CrossRefPubMed

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 11:13–25CrossRefPubMed

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):69–78CrossRefPubMedPubMedCentral

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):273–280CrossRefPubMed

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 10:23–32CrossRefPubMed

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

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 5:5631CrossRefPubMedPubMedCentral

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):315–325CrossRef

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):e29684CrossRefPubMedPubMedCentral

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):170–180CrossRefPubMed

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 12:199–207CrossRefPubMed

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):386–393CrossRefPubMed

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):452–462CrossRefPubMed

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):147CrossRefPubMed

15.

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

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):3555–3563CrossRefPubMed

17.

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

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 17:110–121CrossRefPubMed

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 14:50–60CrossRefPubMed

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 12:144–154CrossRefPubMed

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):1079–1086CrossRef

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 20:20–29CrossRefPubMed

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):18CrossRef

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–D1015CrossRefPubMed

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 19:269–271CrossRefPubMed

26.

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

Title: Case report: on the use of the HID-Ion AmpliSeq™ Ancestry Panel in a real forensic case
Authors: C. Hollard
C. Keyser
T. Delabarde
A. Gonzalez
C. Vilela Lamego
V. Zvénigorosky
B. Ludes
Publication date: 01-03-2017
Publisher: Springer Berlin Heidelberg
Published in: International Journal of Legal Medicine / Issue 2/2017
Print ISSN: 0937-9827
Electronic ISSN: 1437-1596
DOI: https://doi.org/10.1007/s00414-016-1425-1

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

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

Abstract

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 2/2017

Blood identification and discrimination between human and nonhuman blood using portable Raman spectroscopy

The circles of life: age at death estimation in burnt teeth through tooth cementum annulations

Characterization of degradation and heterozygote balance by simulation of the forensic DNA analysis process

Dental age estimation in the living after completion of third molar mineralization: new data for Gustafson’s criteria

New approach to age estimation of male and female adult skeletons based on the morphological characteristics of the acetabulum

Anterior wrist and medial malleolus: the optimal sites for tissue selection in electric death through hand-to-foot circuit pathway