Juliana Gozi de Aquino1, Luz Adriana Pérez2, Helena Groot2, Maria Claudia Lattig2,Elizeu Fagundes de Carvalho1, Leonor Gusmão1,3
1DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Brazil;
2Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia;
3IPATIMUP (Institute of Patology and Molecular Imunology from Univ.of Porto), Portugal.
Introduction
The study of the genetic variation of different polymorphisms that are present in the genome has contributed to a better understanding of human populations’ history, namely by disclosing aspects related to the ancestry of different groups throughout the world. Markers with moderate mutation rates are less prone to present alleles that are identical by state rather than by descent, and are more likely to present higher differences in allele frequencies between populations, being suitable ancestry informative markers (AIM) [1-5]. In forensic genetics, for database purposes, it is important to know the genetic background of a country and take into account population stratification events. Most countries in South America present substructure due to different admixture events along the countries, as it is the case of Brazil and Colombia [6,7]. The study of AIMs can be very helpful to disclose these admixture patterns.
AIMs can also be used in forensic with the objective of determining the possible population of origin of the donor of a sample in a crime scenario with no suspects. In some situations, information based on highly polymorphic STR and SNP markers, with low levels of variation among populations, is available and used to make inferences about individuals’ ancestry in forensic casework. Although this type of markers is not adequate to give precise estimates of ancestry, it is expected to obtain some hints about the population of origin of a suspect [9, 10, 11]. Nevertheless, the error associated to the use of other type of markers than AIM is usually unknown. The aim of this study was to evaluate the performance of a set of markers that were designed for human identification when applied to estimate individual ancestry. The genetic polymorphisms utilized in this study are Indels located on autosomes, since they combine interesting features of other markers as a wide dispersion along the genome, the availability of
multiplex systems able to amplify many loci simultaneously, and simple laboratory genotyping methodologies [12,13,14,15].
With this purpose, father-mother-son trios with paternity confirmed were selected and analyzed through a genotyping methodology described using 38 INDELs markers in a single multiplex PCR. The results obtained were compared with proportions of components ancestry obtained when was utilized a multiplex constituted for 46 informative markers of ancestry.
The values observed for admixture proportions in each son were compared with the values expected considering the parent’s ancestry.
Materials and Methods
Results and Discussion
Inferring genetic ancestry in the fathers and mothers
Ancestry proportions were calculated using the ID-Indel and the AIM-Indel multiplex marker sets, in the two population samples of unrelated individuals (fathers and mothers) from Colombia and Brazil. The results showed a prevalent proportion of European and Native American contributions to the Colombia sample, and higher African and European contributions to the sample from Brazil (Table 1).
Amplification
Genotyping Electropherograms
using the software GeneMapper ID v4.1
DNA extraction DNA
samples
Statistical data analyses: Software
Structure v2.3.3
Table 1: Proportions of ancestry obtained in Brazil and Colombia samples for the tree Continental groups (Africans, Europeans and Native Americans).
Different ancestry estimates were obtained when using the AIM-Indel or the ID-Indel multiplexes, both in the Brazilian and in the Colombian samples. One interesting finding was a trend for higher differences in the ancestry component with the lower proportion. Thus, in Brazil, a variation from 10.90% to 22.20% Native American contribution was observed when using the AIM-Indels and the ID-Indels, respectively. In contrast, the African contribution to the Colombian sample showed the highest differences, varying from 7.41% and 21.70%, for the AIM-Indels and the ID-Indels, respectively.
Inferring genetic ancestry in trios
In the investigation involving father-mother-son trios, in a population in equilibrium it is expected that the genetic ancestry of a child results from the average ancestry calculated for both parents. Therefore, for a group of markers that accurately represents individual ancestry, differences between the ancestry values observed in an individual (observed values) and those calculated as the average values from his parents (expected value) should be low. The observed and expected ancestry values obtained for the 30 children from Brasil and Colombia are represented in figures 1 and 2, when using the AIM-Indels and ID-Indels, respectively.
Figure 1: Proportion of ancestry in children using the AIM-Indels multiplex: expected value (yellow bars) vs. observed value (blue bars).
Figure 2: Proportion of ancestry in children using the ID-Indels multiplex: expected value (blue bars) vs. observed value (red bars).
Relative proportions of ancestry
The absolute/relative differences between the expected and observed values of ancestry obtained when genotyping the sons were calculated for both multiplex and the results are presented in figure 3.
Figure 3: Relative differences on observed and expected proportions of ancestry estimated in the sons. (A) represent the values obtained for AIM-Indel, (B) represents those obtained with ID-Indel.
Conclusion
According to the results, we observe a trend to larger errors in ancestry components of smaller proportion: the African component in Colombia (29% against 36%) and the Native American component in Brazil (37% against 20%), both for AIM-Indels and ID-Indels. In summary, larger errors are observed in the ancestry components that are less represented in the populations. Additionally, in the results analyzed, no significant differences were observed between the ancestral proportions obtained using the “Admixture Model” or the “Use PopInfo Model”. Finally, the same samples were further analyzed with the purpose of evaluating possible differences among the two models that use correlated or independent allele frequencies, and similar results were obtained for these two different methods, with differences lower than 1%.
Acknowledgments
Financial support was granted by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and DNA program – State University and Justice Court of Rio de Janeiro, Brazil. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by the Portuguese Foundation for Science and Technology (FCT).
References
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3.1.2 Avaliando a capacidade de diferentes conjuntos de Indels para estimativa de ancestralidade
Comunicação apresentada em congresso internacional e artigo completo publicado nos anais do congresso:
Comunicação: Assessing the suitability of different sets of Indels in ancestry estimation 26th Congress of the International Society for Forensic Genetics (ISFG) – Cracóvia, 2015
Artigo I: Assessing the suitability of different sets of Indels in ancestry estimation