Genetic structure characterization of Chileans reflects historical immigration patterns

Abstract

Identifying the ancestral components of genomes of admixed individuals helps uncovering the genetic basis of diseases and understanding the demographic history of populations. We estimate local ancestry on 313 Chileans and assess the contribution from three continental populations. The distribution of ancestry block-length suggests an average admixing time around 10 generations ago. Sex-chromosome analyses confirm imbalanced contribution of European men and Native-American women. Previously known genes under selection contain SNPs showing large difference in allele frequencies. Furthermore, we show that assessing ancestry is harder at SNPs with higher recombination rates and easier at SNPs with large difference in allele frequencies at the ancestral populations. Two observations, that African ancestry proportions systematically decrease from North to South, and that European ancestry proportions are highest in central regions, show that the genetic structure of Chileans is under the influence of a diffusion process leading to an ancestry gradient related to geography.

Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations

“…Latin America | population genetics | Salvador SCAALA | Bambuí Cohort Study of Ageing | Pelotas Birth Cohort Study L atin Americans, who are classical models of the effects of admixture in human populations (1,2), remain underrepresented in studies of human genomic diversity, notwithstanding recent studies (3,4). Indeed, no large genome-wide study on admixed South Americans has been conducted so far.…”

“…PCAdmix infers the ancestry of each window. Local ancestry inferences were performed after linked markers (r 2 > 0.99) were pruned to avoid ancestry misestimating caused by overfitting (4). We considered only the windows in which ancestry was inferred by the forwardbackward algorithm with a posterior probability >0.90.…”

Characterization of the CYP2D6 drug metabolizing phenotypes of the Chilean mestizo population through polymorphism analyses

“…The lack of the *17 is expected since it is frequent among African populations (34%) but is typically not present among Caucasian populations [31]. While there is African ancestry in the Chilean admixed population, the proportion is very low [24].…”

“…The protocol was approved by the Ethics Committee for Human Research at the Faculty of Medicine, University of Chile. The Amerindian-Caucasian admixture was determined to be 18%using ABO blood group distribution (BioClone ® , ABO Pharmaceuticals, EE.UU) the Hardy-Weinberg and Bernstein equation [22][23][24].…”

Caracterización de una muestra de pacientes chilenos con periodontitis y frecuencia del polimorfismo H131R en el receptor FcγRIIa.

“…Estas últimas se evidencian al comparar las frecuencias genotípicas de homocigotos R/R (como ejemplo) en poblaciones sin enfermedad: 23% en la población caucásica, 31% en población nativa norte-americana y 6% en población japonesa y china (13) . En este contexto, cabe destacar que nuestra población es reconocidamente una mezcla entre los pueblos originarios e inmigrantes europeos, demostrándose recientemente que un chileno promedio está constituido por un 44,7% de genes nativos americanos, 52,3% europeos y 3,0% africanos (51) . En conclusión, este es el primer trabajo en que se estudia el polimorfismo H131R en el Fc RIIa en población chilena en una muestra de pacientes adecuadamente caracterizados, utilizando parámetros clínicos claros que hoy en día están ampliamente validados en la literatura.…”