Can Ancestry SNPs Generate Investigative Leads?

You have a crime scene sample, extracted plenty of DNA, and searched the sample profile against your national DNA database – you’ve received no hits… nothing at all. For many casework labs, the lack of a match is potentially a stopping point in the investigation. Now what’s the next step? First, let’s think about AIMs. Ancestry Informative Markers are SNPs that are scattered across the genome with different frequencies among various populations¹ and can be used to assess the biogeographic origins of an individual. Add to that the ability to multiplex and analyze hundreds of such SNPs in a single reaction using massively parallel sequencing (MPS). Now forensic DNA analysts have an avenue for generating investigative leads for their law enforcement partners.

The Applied Biosystems™ Precision ID Ancestry Panel includes 165 autosomal markers that provide biogeographic ancestry information. Fifty-five of these markers were selected based on a publication by Dr. Kenneth Kidd² , and 123 markers were selected based on a publication by Dr. Michael Seldin³. These amplicons are all <130 bases in length which makes them ideal for analyzing degraded samples. Let’s take a look at how this approach is being used to evaluate samples and populations from around the globe.

mtDNA + Y-STRs + piSNPs + AIMs = Biogeographical Ancestry of a Carbonized Corpse

An unidentified adult male body was found in Paris (2014) but no further information could be determined. There were no matching dental records, an STR profile did not generate a match to any database and all personal belongings found were charred. The French authorities then approved the use of additional genetic analyses. Hollard, C., et al devised a strategy to analyze mtDNA for maternal lineage, Y-STRs for paternal lineage, AIMs for additional elucidation of biogeographic ancestry and phenotypic SNPs for physical traits. The combined results from all these tests indicated an individual from either the Mediterranean Basin or Southwest Asia. The mtDNA haplotype from EMPOP was HV0, found primarily in west Eurasian populations, the Y-STR profile was E1b1b with a match in 2 Tunisian individuals, piSNP showed a 95% chance of having brown eyes, and AIMs results from Precision ID Ancestry Panel and HID SNP Genotyper showed ancestry from southwest Asia and Mediterranean regions. The admixture analysis from the two subpanels showed slightly different results, likely due to the available underlying populations. According to the authors “…this work has already provided elements that are useful to the progress of the investigation and it also highlighted specific issues that will arise in concrete forensic cases⁴.

First Step for Using Ancestry Inference in Crime Labs

The Section of Forensic Genetics at the University of Copenhagen recently published their validation of identity SNP usage in their crime laboratory. They’ve now begun to establish the parameters needed to use ancestry SNPs as well. In Pereira,V et al, the team has evaluated parameters such as locus balance, heterozygote balance and noise level in the Precision ID Ancestry Panel and set their analysis criteria accordingly. In this study, the team analyzed DNA from 142 subjects of Danish ancestry, 98 individuals from Somalia and included data from a previous study of 77 individuals from Greenland⁵. They include a material and methods section that describes their changes to standard protocol and describe why they have chosen to eliminate 3 SNPs from the final analysis. This study stresses the importance of using suitable reference populations to infer ancestry, particularly populations with admixture⁶.

Custom Panel Design Tailored to Your Regional Needs

The EUROFORGEN consortium has designed a new global ancestry informative SNP panel using the Ion AmpliSeq™ design pipeline. Eduardoff, M. et al originally designed a panel consisting of 128 SNPs, of which 125 performed well for a first-time conversion rate of 97.6%. For the three SNP assays that underperformed, two of them were replaced with new assays. After evaluation of the primers, the group recommends pre-selection of markers that avoid homopolymer content and indels in the flanking sequence as a key to success. In this study, the group tested inter-laboratory performance across five sites that included sequencing performance on the Ion PGM™ System, sensitivity analysis via serial dilution and use of degraded DNA samples, and mixture detection. The results for the 14 study populations, across the five major continental populations, showed very good results for group differentiation and admixture detection. However south Asian populations were not well discriminated and additional markers specific to those populations are being sourced⁷.

More and more labs are investigating how they can implement targeted sequencing of ancestry informative SNPs using MPS to help solve more crimes. Whether it’s an off-the-shelf panel or one designed especially for your geographic region, the Precision ID NGS System for human identification offers flexibility and simplicity for your applications. Dr. Soizic Le-Gunier from IGNA in France has discussed how SNP genotyping will have an impact in the future.

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