Evaluating the effect of marker panel sizes on estimation of bio-geographical co-ancestry proportions

A large number of ancestry-informative marker panels have been developed for forensic bio-geographical ancestry (BGA) analysis during the past decade, which offer valuable investigative tools for cold cases. The developed assays for capillary electrophoresis (CE) and massively parallel sequencing (MPS) focus on the differentiation of major populations, with MPS allowing larger numbers of markers that can be multiplexed at the same time and therefore improved differentiation of more closely related Eurasian populations. One limitation of BGA inference tools is the handling of co-ancestry in individuals with admixted backgrounds, which leads to two situations being indistinguishable: (i) the individual belongs to an admixed population, or (ii) the individual has recent ancestors from different populations. Accurate and precise co-ancestry estimates can help, as first or second-degree admixture would show a ∼ 50-50 % or ∼ 75-25 % ratio of co-ancestry proportions. Here we compared the co-ancestry proportion estimations obtained for the set of 2504 individuals from the 1000 Genomes Project with dedicated BGA and human identification (ID) assays of different sizes compared to those obtained with the > 500,000 SNP Affymetrix Human Origins panel as the point of reference for each individual. The results of the correlation analysis performed with > 500 admixed individuals indicate that panel size plays a major role in the accuracy of the co-ancestry estimates. Therefore, the large-scale forensic MPS ID panels we evaluated constitute a valuable alternative to small- and medium-scale BGA panels, especially when admixture is expected.