The SNPforID 34-plex—Its ability to infer level of admixture in individuals
Introduction
At present, forensic scientists mainly focus on using individualization markers, such as short tandem repeats, to include or exclude persons of interest in criminal investigations. This approach however does not advance investigations when there are no suspect(s) due to absence of database matches, eye-witnesses, and general crime circumstances. In such cases, inference of the biogeographical ancestry of the crime scene sample can be a valuable tool providing important investigative leads. The SNPforID 34-plex was designed to predict biogeographical ancestry from three geographic regions (Africa, Europe and East Asia) using 34 autosomal single nucleotide polymorphisms (SNPs) [1], [2]. This system has been used to infer biogeographical ancestry in samples from unknown donors [3], but its ability to predict ancestry in individuals with known levels of admixture has not been assessed.
Section snippets
Materials and methods
Buccal swab and mouthwash samples were obtained from 56 admixed individuals belonging to 15 families reflecting a genealogy ranging from first to fourth generation, since initial Asian/European admixture. All participants completed a questionnaire including information about their ancestry for two previous generations and assisted the researchers in the construction of a family pedigree as far as four previous generations.
DNA was extracted using DNA IQ™ (Promega, USA) and quantitated using
Results
Overall, allele genotyping success rate was over 99% and comparative population contribution using STRUCTURE was analyzed for all samples. The average ± SD contribution from Asian and European ancestries in individuals self-declared as first generation since admixture (n = 31) was 0.46 ± 0.13 and 0.54 ± 0.13, respectively (Fig. 1). As expected, the observed average ± SD European contribution increased in individuals of 1/4 (n = 8), 1/8 (n = 9) and 1/16 (n = 8) Asian/European ancestries – 0.78/0.13, 0.89/0.05
Conclusions
Even though the SNPforID employs a relatively small number of autosomal SNPs to infer biogeographical ancestry, our results suggest it can be a reliable tool to infer levels of admixture within individuals. However, challenging samples, such as mixtures, degraded samples and/or samples of individuals with complex ancestry admixture, must be investigated with caution as previously demonstrated [3].
A larger set of relevant markers could offer a more reliable inference of ancestry and levels of
Role of funding
Financial support was provided to PRP by La Trobe University through LTUFRRS and LTUPRS awards. C.S. is supported by a Ph.D. Grant (SFRH/BD/75627/2010) awarded by the Portuguese Foundation for Science and Technology and co-financed by the European Social Fund (Human Potential Thematic Operational Program).
Conflict of interest
None.
Acknowledgements
The authors would like to thank the volunteers for participating in this study and staff and students from VPFSD and LTU for productive scientific discussions and technical support. We would also like to thank our colleagues from Santiago de Compostela (Spain) for providing the SNPforID assays.
References (4)
Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs
Forensic Sci. Int. Genet.
(2007)Revision of the SNPforID 34-plex forensic ancestry test: assay enhancements, standard reference sample genotypes and extended population studies
Forensic Sci. Int. Genet.
(2013)
Cited by (4)
Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets
2015, Legal MedicineCitation Excerpt :Analysis within the Thai population (excluding CE_THA and NE_THA) using 273 AIMs (PC1 = 4.9%, PC2 = 3.4%), visibly differentiated between a northern (THA-NOR) and southern (THA-SOU) Thai population (Fig. 2.3). The developing panel of individualized and ancestry informative SNPs was introduced in the forensic community within the past few years [8–11]. In earlier studies, a 128-SNP panel was demonstrated to have the capability to cluster continentals corresponding to European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican [21] ancestry.
A multiple predictive tool approach for phenotypic and biogeographical ancestry inferences
2022, Journal of the Canadian Society of Forensic SciencePredicting biogeographical ancestry in admixed individuals - Values and limitations of using uniparental and autosomal markers
2016, Australian Journal of Forensic Sciences