Straightforward Inference of Ancestry and Admixture Proportions through Ancestry-Informative Insertion Deletion Multiplexing

Abstract

Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies.This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach.HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level.In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.

Optimization of a pentaplex panel for MSI analysis without control DNA in a Brazilian population: correlation with ancestry markers

“…33,37 We concluded that this panel has accuracy and is suitable to estimate genetic ancestry in highly admixed populations such as the Brazilian. 33,37 Herein, we aimed to establish the QMVR of BAT-25, BAT-26, NR-21, NR-24, and NR-27 markers, in a Brazilian healthy population, to evaluate the feasibility of MSI status determination of tumors without the need of matching normal DNA. Furthermore, we intend to determine the ancestry of Brazilian individuals using specific AIMINDELs and correlate with their QMVR.…”

“…[33][34][35][36] Some of these studies are focused on insertion deletion polymorphisms (INDELs) that are likely to be important factors underlying inherited traits in humans. 33 Recently, using a set of AIM-INDELs, we estimated the ancestry proportions of individuals from Amazonas, Belém, and Rio de Janeiro populations in Brazil. 33,37 We concluded that this panel has accuracy and is suitable to estimate genetic ancestry in highly admixed populations such as the Brazilian.…”

“…33 Recently, using a set of AIM-INDELs, we estimated the ancestry proportions of individuals from Amazonas, Belém, and Rio de Janeiro populations in Brazil. 33,37 We concluded that this panel has accuracy and is suitable to estimate genetic ancestry in highly admixed populations such as the Brazilian. 33,37 Herein, we aimed to establish the QMVR of BAT-25, BAT-26, NR-21, NR-24, and NR-27 markers, in a Brazilian healthy population, to evaluate the feasibility of MSI status determination of tumors without the need of matching normal DNA.…”

Study of InDel genetic markers with forensic and ancestry informative interest in PALOP’s immigrant populations in Lisboa

“…Significative differences in allele frequencies of InDel markers, between different groups or populations, can be used as ancestry and eventually, evolutionary indicators [13]. [14,15].…”

Revisión sobre los marcadores del origen biogeográfico y su aplicación en la investigación forense

“…La simplicidad de este enfoque proporciona un uso fácil y una elevada eficiencia en tiempo y coste [14]. Estos marcadores son capaces de distinguir de modo fiable la ancestralidad entre las principales poblaciones continentales de África, Europa, este de Asia y América [16]. Por último, proporcionan una capacidad superior para detectar mezclas de adn de individuos distintos, dado que en los electroferogramas producen patrones de picos mucho más equilibrados que los snp.…”