Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing

Abstract

There is growing interest in developing additional DNA typing techniques to provide better investigative leads in forensic analysis. These include inference of genetic ancestry and prediction of common physical characteristics of DNA donors. To date, forensic ancestry analysis has centered on population-divergent SNPs but these binary loci cannot reliably detect DNA mixtures, common in forensic samples. Furthermore, STR genotypes, forming the principal DNA profiling system, are not routinely combined with forensic SNPs to strengthen frequency data available for ancestry inference. We report development of a 12-STR multiplex composed of ancestry informative marker STRs (AIM-STRs) selected from 434 tetranucleotide repeat loci. We adapted our online Bayesian classifier for AIM-SNPs: Snipper, to handle multiallele STR data using frequency-based training sets. We assessed the ability of the 12-plex AIM-STRs to differentiate CEPH Human Genome Diversity Panel populations, plus their informativeness combined with established forensic STRs and AIM-SNPs. We found combining STRs and SNPs improves the success rate of ancestry assignments while providing a reliable mixture detection system lacking from SNP analysis alone. As the 12 STRs generally show a broad range of alleles in all populations, they provide highly informative supplementary STRs for extended relationship testing and identification of missing persons with incomplete reference pedigrees. Lastly, mixed marker approaches (combining STRs with binary loci) for simple ancestry inference tests beyond forensic analysis bring advantages and we discuss the genotyping options available.

A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set

“…However, at least two main difficulties are imposed in applying these panels in a new study sample, (1) AIMs such as insertion-deletion [5][6][7] or microsatellite markers 13 are difficult to multiplex, need primer design by the developers and standardization of PCR conditions, hindering the access and reproduction in large samples. If the AIMs are SNPs, another difficulty (also present in the first case) is (2) the adequacy of reference ancestral populations used in AIMs selection and its effect on ancestry estimates for the specific population to be studied.…”

Revisión sobre los marcadores del origen biogeográfico y su aplicación en la investigación forense

“…En relación con los str, se han realizado algunos intentos pero siempre en conjunción con los snp [14]. Un conjunto de str que refleje el origen geográfico de un individuo es difícil de definir debido al multialelismo y a la hipervariabilidad.…”

“…Los snp son polimorfismos de secuencia, por lo cual para conocer la posición polimórfica se hace necesario secuenciar; mientras que los InDels son polimorfismos de longitud, con lo que tan solo se debe conocer su diferencia en el tamaño del fragmento. La simplicidad de este enfoque proporciona un uso fácil y una elevada eficiencia en tiempo y coste [14]. Estos marcadores son capaces de distinguir de modo fiable la ancestralidad entre las principales poblaciones continentales de África, Europa, este de Asia y América [16].…”

Inference of Ancestry in Forensic Analysis I: Autosomal Ancestry-Informative Marker Sets

“…A complimentary SNaPshot forensic ancestry test has also been developed to use alongside 34-plex termed Eurasiaplex : designed to differentiate South Asians from Europeans [ 8 ]. Potentially more useful for forensic geneticists interested in analyzing ancestry with tests as straightforward as routine DNA profi ling, SNaPshot tests have now also been extended with ancestry-informative insertion-deletion marker sets (AIM-Indels) [ 9 , 10 ] and ancestry-informative STR ( AIM-STR) sets [ 11 ]. Since both marker sets are typed using dye-labeled PCR primers and tests place PCR amplifi cation products directly into capillary electrophoresis (direct PCR-to-CE), the peak balance obtained is much better than SNaPshot such that electrophoretic signals more directly refl ect the allelic ratios of input DNA.…”

“…The major advantage of direct PCR-to-CE is that a single reaction step restores the simple relationship between allele peak height ratios and input DNA-making mixture detection more reliable than when using SNaPshot [ 12 ]. The ancestry-informative Indels we identifi ed were collected into a 46-plex assay designed to provide differentiation of Africans, Europeans, East Asians, and Native Americans [ 11 ]. 4.…”