Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations

Abstract

The EUROFORGEN NAME panel is a second-tier ancestry panel designed to differentiate individuals from the Middle East, North Africa, and Europe. The first version of the panel was developed for the MassARRAY® system and included 111 SNPs. Here, a custom AmpliSeq™ EUROFORGEN NAME panel with 102 of the original 111 loci was used to sequence 1,098 individuals from 14 populations from Europe, the Middle East, North Africa, North-East Africa, and South-Central Asia. These samples were also sequenced with the first-tier Precision ID Ancestry Panel. The GenoGeographer software was used to assign the AIM profiles to reference populations and calculate the weight of the evidence as likelihood ratios. The combination of the EUROFORGEN NAME and Precision ID Ancestry panels led to fewer ambiguous assignments, especially for individuals from the Middle East and South-Central Asia. The likelihood ratios showed that North African individuals could be separated from European and Middle Eastern individuals using the Precision ID Ancestry Panel. The separation improved with the addition of the EUROFORGEN NAME panel. The analyses also showed that the separation of Middle Eastern populations from European and South-Central Asian populations was challenging even when both panels were applied.

Estimating individual admixture from finite reference databases

“…see that European and Middle-East ancestry is in some cases hard to distinguish, see e.g. Figure 2(C)), a fact which is known from the literature (Truelsen et al, 2021). Technically, our analysis of the approximative normality of the Maximum-Likelihood estimator (Theorem 2) is dealing with a simplified population model, where geographic origins of individuals from the reference database are known.…”