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Iannacone G.C.,Institute of Legal Medicine and Forensic science
Forensic Science International: Genetics Supplement Series | Year: 2015

During the DNA identification process of 15000 missing persons in Peru between 1980 and 2000, we observed many cases of random matches due to the population genetic structure (founder effect, low gene flow between communities and inbreeding). In this genetic context, since 2002, we have been developing an algorithm named ALIGEN with the aim of improving the match and identification. This algorithm performs a meiosis simulation in two DNA databases (relatives and missing persons). In each DNA database ALIGEN generated the haploid profiles (hap-file) for each genetic profile divided in five groups of four STR markers (match group) with a total of twenty STR markers. Simultaneously, we performs a kinship analysis using the model of allele Identity by descendent (IBD) using a threshold of 90% posterior probability in the case of fullsibs with the aim to obtain only the significative relationship and avoiding the random matches. To support the first analysis, the algorithm generated a genetic distances between two genetic profile using hap-file and this form the matrix of likeness that correspond to the genetic distance among all genetic profiles (relatives and missing persons). This matrix is used in MEGA with the aim to obtain a relationship tree. In this way we can confirm the matches, the random matches and evidence of unknown relationships. Other characteristic of the algorithm, it can able to ensure the DNA information privacy through the encryption of each genetic profile using a Hash encryption model with de hap-file generated and it is a criteria very important in the future of populations DNA databasing. Finally, ALIGEN have been validated in the last 13 years solving the identification of missing persons in many cases at national and international level. For this raison, we wish share this algorithm as an easy tool that it can be implementing for any laboratory using the formulas described in this article. © 2015 Elsevier Ireland Ltd. Source

Ibarra A.,University of Antioquia | Freire-Aradas A.,University of Santiago de Compostela | Martinez M.,University of Antioquia | Fondevila M.,University of Santiago de Compostela | And 8 more authors.
International Journal of Legal Medicine | Year: 2014

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. © 2013 Springer-Verlag Berlin Heidelberg. Source

Ibarra A.,University of Antioquia | Restrepo T.,University of Antioquia | Rojas W.,University of Antioquia | Castillo A.,Industrial University of Santander | And 10 more authors.
PLoS ONE | Year: 2014

The European and African contribution to the pre-existing Native American background has influenced the complex genetic pool of Colombia. Because colonisation was not homogeneous in this country, current populations are, therefore, expected to have different proportions of Native American, European and African ancestral contributions. The aim of this work was to examine 11 urban admixed populations and a Native American group, called Pastos, for 32 X chromosome indel markers to expand the current knowledge concerning the genetic background of Colombia. The results revealed a highly diverse genetic background comprising all admixed populations, harbouring important X chromosome contributions from all continental source populations. In addition, Colombia is genetically sub-structured, with different proportions of European and African influxes depending on the regions. The samples from the North Pacific and Caribbean coasts have a high African ancestry, showing the highest levels of diversity. The sample from the South Andean region showed the lowest diversity and significantly higher proportion of Native American ancestry than the other samples from the North Pacific and Caribbean coasts, Central-West and Central-East Andean regions, and the Orinoquian region. The results of admixture analysis using X-chromosomal markers suggest that the high proportion of African ancestry in the North Pacific coast was primarily male driven. These men have joined to females with higher Native American and European ancestry (likely resulting from a classic colonial asymmetric mating type: European male x Amerindian female). This high proportion of male-mediated African contributions is atypical of colonial settings, suggesting that the admixture occurred during a period when African people were no longer enslaved. In the remaining regions, the African contribution was primarily female-mediated, whereas the European counterpart was primarily male driven and the Native American ancestry contribution was not gender biased. © 2014 Ibarra et al. Source

Iannacone G.C.,Institute of Legal Medicine and Forensic science | Parra R.,Institute of Legal Medicine and Forensic science | Bermejo M.,Institute of Legal Medicine and Forensic science | Rojas Y.,Institute of Legal Medicine and Forensic science | And 5 more authors.
Forensic Science International: Genetics Supplement Series | Year: 2011

In the process of identifying around 15,000 missing persons by the armed violence in Peru (1980-2000), the major problem is the high probability of random matches in especial of Andean Ayacucho population which represents the largest number of missing persons. To that end, in a first analysis, we analyzed the relationships and genetic structure in 880 individuals from 20 regions of Peru (including Ayacucho) with IDENTIFILER Kit and in a second analysis; we studied 203 individuals of Ayacucho using the ARGUS-X and ESSPLEX_SE Kit with the aim to confirm the intrapopulation structure found in the first analysis. In the first analysis using the delta-mu parameter, clearly shows three genetic groups at the national level (North, Central and South) with a low variability among groups but significative with AMOVA (0.47%** (P< 0.01)). In the tree, Ayacucho population is located in the south group and interestingly showed a significative FIS (0.10** (P< 0.01)). The second analysis confirm this FIS but lowest (FIS = 0.06) and this FIS could be explained by the evidence of a recent bottleneck found under the IAM, SMM and TPM models (P< 0.01). On the other hand, the X-STR show low probability of random match than in Autosomic STR which may be related to content of admixture among native and foreign populations (30% foreign content in Peruvian population). The results in this study are consistent with the demographic history (processes of migration, immigration, inbreeding), which contribute to the increase of IBDs and may be related to the random match DNA identification. © 2011 Elsevier Ireland Ltd. Source

Rothe J.,Institute of Legal Medicine and Forensic science | Nagy M.,Institute of Legal Medicine and Forensic science
Electrophoresis | Year: 2012

Current human genome databases for public single nucleotide polymorphisms (SNPs) still contain a substantial fraction of false entries. The main reasons for errors include sequencing or assembly errors, paralogous sequence-, and private variants. In the course of our studies on the Y chromosome, we established a set of internal laboratory guidelines for reliably identifying false SNP entries in databases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

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