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

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.

Does ethnic ancestry play a role in smoking?

“…Individual interethnic admixtures were determined using a panel of 48-INDELs ancestry-informative-marker (AIM) panel, previously applied for Brazilian population analysis. Genotyping of the 48 INDEL markers in this study followed the methodology described by Santos et al (2010). This approach permitted estimates of individual and global admixture relative to three ancestry groups: European, African Sub-Saharan and Amerindian.…”

“…A set of 48 ancestry-informative insertiondeletion polymorphisms (INDELs) was developed aiming at measuring the proportions of three different ancestries, sub-Saharan African, European, and Amerindian, in mixed populations (Santos et al 2010). This panel allowed accurate estimation of individual and global interethnic admixture relative to the ancestry of Brazilians from three regions of the country.…”

Development of two multiplex mini-sequencing panels of ancestry informative SNPs for studies in Latin Americans: an application to populations of the State of Minas Gerais (Brazil)

“…Kosoy et al (2009) have shown that panels of 24 AIMs are useful to ascertain the origin of subjects from particular continents and to correct for population stratification at the population level. Some low-medium cost multiplex panels of AIMs have been published (Lins et al, 2010;Santos et al, 2010); however, these may vary in their informativeness. Therefore, the best option for an investigator performing an admixture study is to assess which combination of AIMs is most informative for the target population.…”

Reply to Moura et al

“…3 Moura et al refer to results from populations in Columbia, Peru and Puerto Rico as 'the literature' for American populations, but this ignores studies performed in Brazil itself, to which our results are more similar. [4][5][6] The one Brazilian study cited was that of Pena et al 7 We noted in our text that, in contrast to our own sample, this paper uses a sample unlikely to be representative of Ceará state or Fortaleza and includes no pseudoancestors of any kind. This is known to distort ancestry in admixed populations.…”