Dataset Information

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina.

ABSTRACT: Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.

SUBMITTER: Luisi P

PROVIDER: S-EPMC7365470 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina.

Luisi Pierre P García Angelina A Berros Juan Manuel JM Motti Josefina M B JMB Demarchi Darío A DA Alfaro Emma E Aquilano Eliana E Argüelles Carina C Avena Sergio S Bailliet Graciela G Beltramo Julieta J Bravi Claudio M CM Cuello Mariela M Dejean Cristina C Dipierri José Edgardo JE Jurado Medina Laura S LS Lanata José Luis JL Muzzio Marina M Parolin María Laura ML Pauro Maia M Paz Sepúlveda Paula B PB Rodríguez Golpe Daniela D Santos María Rita MR Schwab Marisol M Silvero Natalia N Zubrzycki Jeremias J Ramallo Virginia V Dopazo Hernán H

PloS one 20200716 7

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previous ...[more]

PMID: 32673320

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Project description:For samples of admixed individuals, it is possible to test for both ancestry effects via admixture mapping and genotype effects via association mapping. Here, we describe a joint test called BMIX that combines admixture and association statistics at single markers. We first perform high-density admixture mapping using local ancestry. We then perform association mapping using stratified regression, wherein for each marker genotypes are stratified by local ancestry. In both stages, we use generalized linear models, providing the advantage that the joint test can be used with any phenotype distribution with an appropriate link function. To define the alternative densities for admixture mapping and association mapping, we describe a method based on autocorrelation to empirically estimate the testing burdens of admixture mapping and association mapping. We then describe a joint test that uses the posterior probabilities from admixture mapping as prior probabilities for association mapping, capitalizing on the reduced testing burden of admixture mapping relative to association mapping. By simulation, we show that BMIX is potentially orders-of-magnitude more powerful than the MIX score, which is currently the most powerful frequentist joint test. We illustrate the gain in power through analysis of fasting plasma glucose among 922 unrelated, non-diabetic, admixed African Americans from the Howard University Family Study. We detected loci at 1q24 and 6q26 as genome-wide significant via admixture mapping; both loci have been independently reported from linkage analysis. Using the association data, we resolved the 1q24 signal into two regions. One region, upstream of the gene FAM78B, contains three binding sites for the transcription factor PPARG and two binding sites for HNF1A, both previously implicated in the pathology of type 2 diabetes. The fact that both loci showed ancestry effects may provide novel insight into the genetic architecture of fasting plasma glucose in individuals of African ancestry.

Dataset Information

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina.

Publications

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina.

Similar Datasets

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