Comparison of the genetic background of different Colombian populations using the SNPforID 52plex identification panel

Abstract

Various strategies for analysing SNP markers and genotyping have been published with the goal of obtaining informative profiles from biological samples that contain only small amounts of template and/or degraded DNA. In this study, a multiplex assay of 52 autosomal single-nucleotide polymorphisms (SNPs) was used to analyse 438 individuals from urban populations from different regions of Colombia, as well as a sample of 50 Native American individuals of the Pastos ethnic group from Nariño. To determine if significant differences in these 52 SNPs exist between the distinct regions of Colombia, genetic distance and admixture analyses were performed based on the available data for 17 different Colombian population groups and for population groups from Africa, Europe and America. The results demonstrate significant differences between the populations from the Southwest Andean, Central-West Andean, Central-East Andean, Orinoquian and northern Colombian Pacific Coast regions. Most of the regions exhibited a European and Native American admixture. One exception is the population from the region of Chocó (on the northern Pacific Coast), which exhibits a high proportion of African admixture (54 %). From the observed genetic backgrounds, it is possible to conclude that a single reference database for the entire country would not be suitable for forensic purposes. The allele frequencies and the forensically relevant parameters were calculated for all of the markers in each Colombian region with significant values for the combined matching probability (power of discrimination ≥0.99999999999999990) and the combined probability of exclusion (≥0.9990) in trios that were obtained from all of the population groups.

A new strategy for umbilical cord blood collection developed at the first Colombian public cord blood bank increases total nucleated cell content

“…The World Marrow Donor Association 2014 database reported that, in Colombia, 92.6% of transplanted UCB units are imported through European or North American BM donor registries. Unfortunately, the imported units do not satisfy current HLA matching demands for hematopoietic transplantation, probably due to the multiethnic migration history of the country . Despite the lack of established policy and legislation regarding a national BM donor registry, support from the District and National Governments led to the implementation of a public UCB bank in Colombia.…”

“…to the multiethnic migration history of the country. 34 Despite the lack of established policy and legislation regarding a national BM donor registry, support from the District and National Governments led to the implementation of a public UCB bank in Colombia.…”

Neither self-reported ethnicity nor declared family origin are reliable indicators of genomic ancestry

“…Amerindian ancestry did not influence self-reported ethnicity or declared family origin probably because it was the minor contributor to the genetic background of our populations, finding also described by other authors in distinct Brazilians subpopulations Moura et al 2015). Ancestry stratification of individuals or populations can be achieved by using different strategies such as INDEL or SNPs markers, and different panels have been created for this end (Ibarra et al 2014;Resque et al 2010;Silva et al 2010;Yang et al 2005). INDEL panels have the advantage of reduced cost in comparison to SNPs panels as it allows to genotype several markers in multiplex fashion by a best value.…”

Genetic characterization of an X-STR decaplex system in the State of Mato Grosso, Brazil: distribution, forensic efficiency and population structure

“…Argentina, Costa Rica and Antioquia have a tri-hybrid population and, for autosomal markers, they show marked European ancestry, followed by Native American ancestry, and a smaller percentage of African ancestry. The African ancestry is very small in Argentina (65% E, 4% A, 31% NA [27]) and in Costa Rica (58% E, 4% A, 38% NA [28]), compared with the percentages in Antioquia (44.3% E, 21.1% A, 34.6% NA [29]). For markers of X chromosome, the population of Antioquia carries genetic heritage of 37.5% E, 29% A and 33.5% NA, showing greater European contribution, which is very close to the Native American data [30].…”