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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.


PubMed | Rovira i Virgili University, Institute of Legal Medicine and Forensic Science, University of Borås, Catalan Institute of health and 2 more.
Type: Review | Journal: Scandinavian journal of trauma, resuscitation and emergency medicine | Year: 2016

Cardiovascular diseases are one of the leading causes of death in the industrialized world. Sudden cardiac death is very often the first manifestation of the disease and it occurs in the prehospital setting. The determination of the sudden cardiac death phenotype is challenging. It requires prospective studies in the community including multiple sources of case ascertainment that help to identify the cause and circumstances of death. The aim of the Clinical and Pathological Registry of Tarragona (ReCaPTa) is to study incidence and etiology of Sudden Cardiac Death in the Tarragona region (Catalonia, Spain).ReCaPTa is a population-based registry of OHCA using multiple sources of surveillance. The population base is 511,662. This registry is compiled chronologically in a relational database and it prospectively contains data on all the OHCA attended by the EMS from April 2014 to April 2017. ReCaPTa collects data after each emergency medical assistance using an online application including variables of the onset of symptoms. A quality control is performed and it permits monitoring the percentage of cases included by the emergency crew. Simultaneously, data from the medico-legal autopsies is taken from the Pathology Center of the area. All the examination findings following a specific protocol for the sudden death study are entered into the ReCaPTa database by one trained person. Survivors admitted to hospital are followed up and their clinical variables are collected in each hospital. The primary care researchers analyze the digital clinical records in order to obtain medical background. All the available data will be reviewed after an adjudication process with the aim of identifying all cases of sudden cardiac death.There is a lack of population-based registries including multiple source of surveillance in the Mediterranean area. The ReCaPTa study could provide valuable information to prevent sudden cardiac death and develop new strategies to improve its survival.


Achakzai N.M.,University of Punjab | Rahman Z.,University of Punjab | Shahzad M.S.,University of Punjab | Daud S.,University of Punjab | And 5 more authors.
Forensic Science International: Genetics | Year: 2012

Afghanistan is a landlocked country in the heart of Asia and since the dawn of humankind Afghanistan has faced centuries of turmoil, strife, conflict, warfare, distress, social unrest, difficult climate, harsh terrain and due to its unique geostrategic position in Eurasia which has historically attracted commerce and conflict. It is an important stop along the Silk Road, connecting the far eastern civilizations to the western world. A 5000-year history of constant invasion. Afghanistan has been repeatedly invaded and conquered by rulers and super powers, neighboring interference in this conflict-tattered land for centuries yet rarely leading to the conquest of this rugged and challenging terrain nation. Afghans are not only shepherds, farmers and nomads but also intense fighters and fierce warriors. Currently very limited genetic studies have been performed in Afghan populations. 17 Y chromosomal short tandem repeats (Y-STRs) were analyzed in 125 unrelated Pashtun (in hindi: Pathan) males residing in the Kandahar region of Southern Afghanistan. A total of 92 unique haplotypes were observed. The predominant haplotype reached a frequency of 9.6%. The haplotype diversity was 0.987 and the discrimination capacity 73.6%. Analysis of molecular variance (AMOVA) reveals a considerable regional stratification within the country as well as between different Pashtun (Pathan) groups from Afghanistan, Pakistan and India. © 2011 Elsevier Ireland Ltd.


Rothe J.,Institute of Legal Medicine and Forensic science | Watkins Jr. N.E.,Dna Software, Inc. | Nagy M.,Institute of Legal Medicine and Forensic science
PLoS ONE | Year: 2012

Allele-specific extension reactions (ASERs) use 3′ terminus-specific primers for the selective extension of completely annealed matches by polymerase. The ability of the polymerase to extend non-specific 3′ terminal mismatches leads to a failure of the reaction, a process that is only partly understood and predictable, and often requires time-consuming assay design. In our studies we investigated haplotype-specific extraction (HSE) for the separation of male DNA mixtures. HSE is an ASER and provides the ability to distinguish between diploid chromosomes from one or more individuals. Here, we show that the success of HSE and allele-specific extension depend strongly on the concentration difference between complete match and 3′ terminal mismatch. Using the oligonucleotide-modeling platform Visual Omp, we demonstrated the dependency of the discrimination power of the polymerase on match- and mismatch-target hybridization between different probe lengths. Therefore, the probe specificity in HSE could be predicted by performing a relative comparison of different probe designs with their simulated differences between the duplex concentration of target-probe match and mismatches. We tested this new model for probe design in more than 300 HSE reactions with 137 different probes and obtained an accordance of 88%. © 2012 Rothe et al.


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.


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.


Rothe J.,Institute of Legal Medicine and Forensic science | Roewer L.,Institute of Legal Medicine and Forensic science | Nagy M.,Institute of Legal Medicine and Forensic science
Forensic Science International: Genetics | Year: 2011

In forensic work, the interpretation of DNA profiles becomes complicated when samples contain more than one contributor because the simultaneous amplification of individual identification markers results in mixed profiles. To overcome this problem, we present haplotype-specific extraction (HSE) as a more straightforward method to analyze a DNA mixture. HSE has been developed to clarify ambiguous HLA alleles by separating diploid samples into their haploid components to facilitate HLA typing. We have started to establish new protocols and strategies to adapt HSE for the separation of male DNA mixtures in forensic analysis. First results have shown an improved enrichment of male DNA from a single contributor. We have also evaluated a new, optimized buffer composition by testing different concentrations of its components. Improved separation of a male DNA mixture is detected using AmpFℓSTR® Yfiler short tandem repeat analysis. © 2010 Elsevier Ireland Ltd.


Rothe J.,Institute of Legal Medicine and Forensic science | Nagy M.,Institute of Legal Medicine and Forensic science
Legal Medicine | Year: 2016

One of the most demanding DNA extractions is from bones and teeth due to the robustness of the material and the relatively low DNA content. The greatest challenge is due to the manifold nature of the material, which is defined by various factors, including age, storage, environmental conditions, and contamination with inhibitors. However, most published protocols do not distinguish between different types or qualities of bone material, but are described as being generally applicable. Our laboratory works with two different extraction methods based on silica membranes or the use of silica beads. We compared the amplification success of the two methods from bone samples with different qualities and in the presence of inhibitors. We found that the DNA extraction using the silica membrane method results an in higher DNA yield but also in a higher risk of co-extracting impurities, which can act as inhibitors. In contrast the silica beads method shows decreased co-extraction of inhibitors but also less DNA yield. Related to our own experiences it has to be considered that each bone material should be reviewed independently regarding the analysis and extraction method. Therefore, the most ambitious task is determining the quality of the bone material, which requires substantial experience. © 2016 Elsevier Ireland Ltd


Rothe J.,Institute of Legal Medicine and Forensic science | Nagy M.,Institute of Legal Medicine and Forensic science
Forensic Science International: Genetics | Year: 2015

In forensic analysis, the interpretation of DNA mixtures is the subject of ongoing debate and requires expertise knowledge. Haplotype-specific extraction (HSE) is an alternative method that enables the separation of large chromosome fragments or haplotypes by using magnetic beads in conjunction with allele-specific probes. HSE thus allows physical separation of the components of a DNA mixture. Here, we present the first multiplex HSE separation of a Y-chromosomal haplotype consisting of six Yfiler short tandem repeat markers from a mixture of Male DNA. © 2015 Elsevier Ireland Ltd. All rights reserved.


PubMed | Institute of Legal Medicine and Forensic science
Type: | Journal: Legal medicine (Tokyo, Japan) | Year: 2016

One of the most demanding DNA extractions is from bones and teeth due to the robustness of the material and the relatively low DNA content. The greatest challenge is due to the manifold nature of the material, which is defined by various factors, including age, storage, environmental conditions, and contamination with inhibitors. However, most published protocols do not distinguish between different types or qualities of bone material, but are described as being generally applicable. Our laboratory works with two different extraction methods based on silica membranes or the use of silica beads. We compared the amplification success of the two methods from bone samples with different qualities and in the presence of inhibitors. We found that the DNA extraction using the silica membrane method results an in higher DNA yield but also in a higher risk of co-extracting impurities, which can act as inhibitors. In contrast the silica beads method shows decreased co-extraction of inhibitors but also less DNA yield. Related to our own experiences it has to be considered that each bone material should be reviewed independently regarding the analysis and extraction method. Therefore, the most ambitious task is determining the quality of the bone material, which requires substantial experience.

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