Assessing individual interethnic admixture and population substructure using a 48-insertion-deletion (INSEL) ancestry-informative marker (AIM) panel

TLDR

Estimating ancestry proportions in admixed populations is crucial for population genetics and for detecting substructure effects in case–control association studies. This study selected 48 ancestry‑informative INDELs to efficiently measure sub‑Saharan African, European, and Native American ancestry proportions in mixed populations. The 48 INDELs were genotyped by multiplex PCR and capillary electrophoresis in 593 parental individuals and 380 admixed Brazilians to assess ancestry proportions. The panel accurately estimated ancestry proportions, revealing nearly exclusive European ancestry in southern Brazilians, mixed African–European–Native American ancestry in Amazonian Afro‑descendants, and substantial trihybrid ancestry in Belém, demonstrating its utility for assessing population substructure in Latin American studies.

Abstract

Estimating the proportions of different ancestries in admixed populations is very important in population genetics studies, and it is particularly important for detecting population substructure effects in case-control association studies. In this work, a set of 48 ancestry-informative insertion-deletion polymorphisms (INDELs) were selected with the goal of efficiently measuring the proportions of three different ancestries (sub-Saharan African, European, and Native American) in mixed populations. All selected markers can be easily analyzed via multiplex PCR and detected with standard capillary electrophoresis. A total of 593 unrelated individuals representative of European, African, and Native American parental populations were typed, as were 380 individuals from three Brazilian populations with known admixture patterns. As expected, the interethnic admixture estimates show that individuals from southern Brazil present an almost exclusively European ancestry; Afro-descendant communities in the Amazon region, apart from the major African contribution, present some degree of admixture with Europeans and Native Americans; and a sample from Belém, in the northeastern Amazon, shows a significant contribution of the three ethnic groups, although with a greater European proportion. In summary, a panel of ancestry-informative INDELs was optimized and proven to be a valuable tool for estimating individual and global ancestry proportions in admixed populations. The ability to accurately infer interethnic admixtures highlights the usefulness of this marker set for assessing population substructure in association studies, particularly those conducted in Brazilian and other Latin American populations sharing trihybrid ancestry patterns.