Building a forensic ancestry panel from the ground up: The EUROFORGEN Global AIM-SNP set

Abstract

Emerging next-generation sequencing technologies will enable DNA analyses to add pigmentation predictive and ancestry informative (AIM) SNPs to the range of markers detectable from a single PCR test. This prompted us to re-appraise current forensic and genomics AIM-SNPs and from the best sets, to identify the most divergent markers for a five population group differentiation of Africans, Europeans, East Asians, Native Americans and Oceanians by using our own online genome variation browsers. We prioritized careful balancing of population differentiation across the five group comparisons in order to minimize bias when estimating co-ancestry proportions in individuals with admixed ancestries. The differentiation of European from Middle East or South Asian ancestries was not chosen as a characteristic in order to concentrate on introducing Oceanian differentiation for the first time in a forensic AIM set. We describe a complete set of 128 AIM-SNPs that have near identical population-specific divergence across five continentally defined population groups. The full set can be systematically reduced in size, while preserving the most informative markers and the balance of population-specific divergence in at least four groups. We describe subsets of 88, 55, 28, 20 and 12 AIMs, enabling both new and existing SNP genotyping technologies to exploit the best markers identified for forensic ancestry analysis.

Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™

“…Fig. 4 shows the analysis of these 14 study populations plus 1000 Genomes test populations extended to the additional data released after the first Global AIM-SNPs publication [17]. The average number of pairwise genotype differences between-( Fig.…”

“…The EUROFORGEN Global ancestry-informative single nucleotide polymorphism panel (herein Global AIM-SNPs) comprises 128 markers designed to distinguish the five continental groups outlined above [17]. The Global AIM-SNPs were compiled to provide the key characteristic of a balanced differentiation of each population group, i.e.…”

“…Therefore, in addition to selecting SNPs with optimum properties for a particular forensic test, in this case ancestry analyses [17], very careful scrutiny of flanking sequence characteristics is required to avoid impairing the test's genotyping precision using MPS technology.…”

DNA Methods to Identify Missing Persons

“…Private polymorphisms, for example, tend by their very nature to be so rare that they are unlikely to have wide utility in forensic investigations, whereas more frequently occurring polymorphisms may lack sufficient resolution to any particular population to make an unequivocal assignment. Despite such drawbacks (Rosenberg et al 2003), a number of studies have identified potential ancestry informative marker sets, including those based on SNPs (Phillips et al 2014, Huckins et al 2014, Kidd et al 2011, Lao et al 2006). …”

Single Nucleotide Polymorphisms in Forensic Applications Based on Identification: Review

“…"Euroforgen" olarak isimlendirilen bu genişletilmiş sette Avrupa, Afrika, Doğu Asya ve Okyanusya populasyonları arasında ayrım yapabilmenin mümkün olabileceği belirtilmiştir. 35 Bundan başka, 29 SNP ile oluşturulan "Pacifiplex" set ile de 34-plex sete ek olarak kullanıldığında Avustralya ve Pasifik bölgesi populasyonları arasında ayrım yapılabilmesinin mümkün olabileceği ileri sürülmüştür. 36 Yukarıda sözü edilen SNP setleri dikkate alınarak çeşitli ticari firmalar tarafın-dan kitler hazırlanmıştır.…”