Papers by Carolina Núñez
Forensic science international. Genetics, May 1, 2018
Y-specific short tandem repeat (Y-STR) loci display different mutation rates and consequently are... more Y-specific short tandem repeat (Y-STR) loci display different mutation rates and consequently are suitable for forensic, genealogical, and evolutionary studies that require different levels of timelines and resolution. Recent efforts have focused on implementing Rapidly Mutating (RM) Y-STRs to assess male specific profiles. However, due to their high mutation rate their use in kinship testing or in phylogenetic studies may be less reliable. In the present study, a novel Slowly Mutating Y-STR (SM) panel, including DYS388, DYS426, DYS461 (Y-GATA-A7.2), DYS485, DYS525, and DYS561, has been developed and evaluated in a sample set of 628 unrelated males from different worldwide populations. This panel is reproducible, sensitive, and robust for forensic applications and may be useful in conjunction with the common multiplexes, particularly in exclusion of kinship cases where minimal discrimination is reported employing the rapidly mutating Y-STR systems. Furthermore, SM Y-STR data may be ...
International journal of legal medicine, Jan 22, 2018
In the present study, the genetic variations of 17 X-STR markers (DXS8378, DXS9898, DXS7133, GATA... more In the present study, the genetic variations of 17 X-STR markers (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801, DXS7423, DXS6809, DXS6799, DXS7132, DXS9902, DXS6800, DXS6789, DXS10075, DXS10079, DXS6807, and DXS6803) were analyzed in 139 unrelated individuals in Nabeul, aiming to perform an X-STR database for anthropological and forensic purposes. Our results indicate that DXS6809 was the most polymorphic locus, whereas DXS6807 was the least informative marker. In addition, the obtained values for the statistical parameters of forensic interest, i.e., the power of discrimination in males (PD) and females (PD), as well as the mean exclusion chance in duos (MEC) and trios (MEC) have demonstrated that this panel of 17 X-STRs is highly informative and useful for forensic application and anthropological research. Additionally, pairwise genetic distances based on F were calculated between Nabeul population and other populations extracted from the literature. Genetic distances...
Electrophoresis, Apr 16, 2016
A Y-STR multiplex system has been developed with the purpose of complementing the widely used 17 ... more A Y-STR multiplex system has been developed with the purpose of complementing the widely used 17 Y-STR haplotyping (AmpFlSTR Y Filer® PCR Amplification kit) routinely employed in forensic and population genetic studies. This new multiplex system includes six additional STR loci (DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) to reach the 23 Y-STR of the PowerPlex® Y23 System. In addition, this kit includes the DYS456 and DYS385 loci for traceability purposes. Male samples from 625 individuals from ten worldwide populations were genotyped, including three sample sets from populations previously published with the 17 Y-STR system to expand their current data. Validation studies demonstrated good performance of the panel set in terms of concordance, sensitivity, and stability in the presence of inhibitors and artificially degraded DNA. The results obtained for haplotype diversity and discrimination capacity with this multiplex system were considerably high, providing further evide...
Forensic Science International: Genetics, 2017
The forensic use of X-STRs requires the creation of allele and haplotype frequency databases in t... more The forensic use of X-STRs requires the creation of allele and haplotype frequency databases in the populations where they are going to be used. Recently, an updated Spanish allele and haplotype frequency database for the new 17 X-STR panel has been created, being the only database available up to now for this new multiplex. In order to broaden the forensic applicability of the 17 X-STR panel, 513 individuals from four different populations located on the Atlantic Coast of Europe and North-West Africa have been studied, i.e. Brittany (France), Ireland, northern Portugal, and Casablanca (Morocco). Allele and haplotype frequency databases, as well as parameters of forensic interest for these populations are presented. The obtained results showed that the 17 X-STR panel constitutes a highly discriminative tool for forensic identification and kinship testing in the studied populations. Furthermore, we aimed to study if these populations located on the Atlantic coast actually share alike allele and haplotype frequency distributions since they have experienced genetic exchanges throughout history. This would allow creating larger forensic databases that include several genetically similar populations for its use in forensic casework. For this purpose, pairwise FST genetic distances between the analyzed populations and others from the Atlantic Coast previously studied with the 17 X-STR panel or the ten coincident markers included in the decaplex of the GHEP-ISFG were estimated. Our results suggest that certain nearby populations located on the European Atlantic coast could have underwent episodes of genetic interchange as they have not shown statistically significant differentiation between them. However, the population of Casablanca showed significant differentiation with the majority of the European populations. Likewise, the autochthonous Basque Country and Brittany populations have shown distinctive allele frequency distributions between them. Therefore, these findings seem to support that the use of independent allele and haplotype frequency databases for each population instead of a global database would be more appropriate for forensic purposes.
Forensic Science International: Genetics, 2016
The currently developed 17 X-STR panel (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801... more The currently developed 17 X-STR panel (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801, DXS7423, DXS6809, DXS6799, DXS7132, DXS9902, DXS6800, DXS6789, DXS10075, DXS10079, DXS6807, and DXS6803) offers a highly discriminative tool for forensic identification and kinship testing. With the aim of providing a global Spanish population X-STR database, we present haplotype and allele frequencies and parameters of forensic interest for the 17 X-STR panel obtained from 593 unrelated individuals from Alicante, Aragon, the Basque Country, Andalusia, Galicia, Madrid, and Barcelona that represent the most populated regions of the Spanish Peninsular territory. The seven populations were compared to test possible population genetic substructures. The lack of significant differences among the studied Spanish populations supports the use of the allele and haplotype frequency database presented herein as a global Spanish population sample useful for statistical evaluation in forensic casework. After conducting the LD plots derived from HapMap and pairwise linkage disequilibrium tests, DXS7132, DXS10075, and DXS10079 markers were included in a cluster and haplotype frequencies were calculated. The improvement in the forensic parameters for the Spanish population using 17 X-STRs in comparison to the previous 10 X-STR allele frequencies database is also shown.
PLOS ONE, 2016
La Hoya (Alava, Basque Country) was one of the most important villages of the Late Bronze and Iro... more La Hoya (Alava, Basque Country) was one of the most important villages of the Late Bronze and Iron Ages of the north of the Iberian Peninsula, until it was violently devastated around the 4th century and abandoned in the 3rd century B.C. Archaeological evidences suggest that descendants from La Hoya placed their new settlement in a nearby hill, which gave rise to the current village of Laguardia. In this study, we have traced the genetic imprints of the extinct inhabitants of La Hoya through the analysis of maternal lineages. In particular, we have analyzed the mitochondrial DNA (mtDNA) control region of 41 human remains recovered from the archaeological site for comparison with a sample of 51 individuals from the geographically close present-day population of Laguardia, as well as 56 individuals of the general population of the province of Alava, where the archaeological site and Laguardia village are located. MtDNA haplotypes were successfully obtained in 25 out of 41 ancient samples, and 14 different haplotypes were identified. The major mtDNA subhaplogroups observed in La Hoya were H1, H3, J1 and U5, which show a distinctive frequency pattern in the autochthonous populations of the north of the Iberian Peninsula. Approximate Bayesian Computation analysis was performed to test the most likely model for the local demographic history. The results did not sustain a genealogical continuity between Laguardia and La Hoya at the haplotype level, although factors such as sampling effects, recent admixture events, and genetic bottlenecks need to be considered. Likewise, the highly similar subhaplogroup composition detected between La Hoya and Laguardia and Alava populations do not allow us to reject a maternal genetic continuity in the human groups of the area since at least the Iron Age to present times. Broader analyses, based on a larger collection of samples and genetic markers, would be required to study fine-scale population events in these human groups.
ELECTROPHORESIS, 2016
Currently, two of the most widely used X-chromosome STR (X-STR) multiplexes are composed by 10 (G... more Currently, two of the most widely used X-chromosome STR (X-STR) multiplexes are composed by 10 (GHEP-ISFG decaplex) and 12 markers (Investigator Argus X-12 Kit). The number of markers included is a drawback for complex relative testing cases, likewise the large size of some amplicons difficult their application to degraded samples. Here, we present a new multiplex of 17 X-STRs with the aim of increasing both the resolution power and forensic applicability. This newly proposed set includes the X-STRs of the GHEP-ISFG decaplex, three X-STRs from the Investigator Argus X-12 Kit, two of them also included in the decaplex, and six additional more. In order to ensure the allele designation, an allelic ladder was developed. The validation of the present multiplex was carried out according to the revised guidelines by the SWGDAM (Scientific Working Group on DNA Analysis Methods). A total of 488 unrelated individuals from four different continents were analyzed. The forensic efficiency evaluation showed high values of combined power of discrimination in males (≥0.999999996) and females (≥0.999999999999995) as well as combined paternity exclusion probabilities in trios (≥0.99999998) and duos (≥0.999996). The results presented herein have demonstrated that the new 17 X-STR set constitutes a high-resolution alternative to the current X-STR multiplexes. This article is protected by copyright. All rights reserved.
PLOS ONE, 2015
The Basque Diaspora in Western USA and Argentina represents two populations which have maintained... more The Basque Diaspora in Western USA and Argentina represents two populations which have maintained strong Basque cultural and social roots in a completely different geographic context. Hence, they provide an exceptional opportunity to study the maternal genetic legacy from the ancestral Basque population and assess the degree of genetic introgression from the host populations in two of the largest Basque communities outside the Basque Country. For this purpose, we analyzed the complete mitochondrial DNA control region of Basque descendants living in Western USA (n = 175) and in Argentina (n = 194). The Diaspora populations studied here displayed a genetic diversity in their European maternal input which was similar to that of the Basque source populations, indicating that not important founder effects would have occurred. Actually, the genetic legacy of the Basque population still prevailed in their present-day maternal pools, by means of a haplogroup distribution similar to the source population characterized by the presence of autochthonous Basque lineages, such as U5b1f1a and J1c5c1. However, introgression of non-Basque lineages, mostly Native American, has been observed in the Diaspora populations, particularly in Argentina, where the quick assimilation of the newcomers would have favored a wider admixture with host populations. In contrast, a longer isolation of the Diaspora groups in USA, because of language and cultural differences, would have limited the introgression of local lineages. This study reveals important differences in the maternal evolutionary histories of these Basque Diaspora populations, which have to be taken into consideration in forensic and medical genetic studies.
Forensic Science International: Genetics Supplement Series, 2015
The use of STRs located in the X chromosome (X-STRs) is very efficient for determining kinship be... more The use of STRs located in the X chromosome (X-STRs) is very efficient for determining kinship between fathers and daughters as well as other complex kinship cases. Currently, X-STR markers are analyzed by using two different multiplexes, the decaplex of the GHEP-ISFG and the Investigator Argus X-12 Kit. Here, we present a new multiplex whose advantage is the analysis of 17 X-STRs in a single reaction. Population samples from four different continents were analyzed. A sensitivity test showed the efficacy of this new multiplex for samples with DNA quantities as low as 100 pg.
Forensic Science International: Genetics Supplement Series, 2015
Forensic Science International: Genetics, 2015
The Spanish Civil War (1936-1939) and posterior dictatorship (until 1970s) stands as one of the m... more The Spanish Civil War (1936-1939) and posterior dictatorship (until 1970s) stands as one of the major conflicts in the recent history of Spain. It led to nearly two hundred thousand men and women executed or murdered extra-judicially or after dubious legal procedures. Nowadays, most of them remain unidentified or even buried in irretraceable mass graves across Spain. Here, we present the genetic identification of human remains found in 26 mass graves located in Northern Spain. A total of 252 post-mortem remains were analyzed and compared to 186 relatives, allowing the identification of 87 victims. Overall, a significant success of DNA profiling was reached, since informative profiles (≥12 STRs and/or mitochondrial DNA profile) were obtained in 85.71% of the remains. This high performance in DNA profiling from challenging samples demonstrated the efficacy of DNA extraction and amplification methods used herein, given that only around 14.29% of the samples did not provide an informative genetic profile for the analysis performed, probably due to the presence of degraded and/or limited DNA in these remains. However, this study shows a partial identification success rate, which is clearly a consequence of the lack of both appropriate family members for genetic comparisons and accurate information about the victims' location. Hence, further perseverance in the exhumation of other intact graves as well as in the search of more alleged relatives is crucial in order to facilitate and increase the number of genetic identifications.
Forensic Science International: Genetics, 2015
Forensic Science International: Genetics, 2015
In order to evaluate the forensic utility of the new PowerPlex(®) Y23 System, two Northern Spanis... more In order to evaluate the forensic utility of the new PowerPlex(®) Y23 System, two Northern Spanish populations, the autochthonous Basque Country (N=105) and Cantabria (N=98), were typed. Two of the new markers incorporated in the panel, the rapid mutating loci DYS576 and DYS570, were among the most discriminative markers in both population datasets. In terms of the analysis of 23 Y-STRs, the two populations showed high haplotype diversities, with values slightly superior in the population of Cantabria (1±0.0015) than in the Basque Country (0.9987±0.0016). The comparison of the discrimination capacity obtained with the analysis of 23 Y-STRs and other available markers sets of 12 Y-STRs (PowerPlex(®) Y System) or 17 Y-STRs (YFiler™), clearly demonstrated an improvement in the population of the Basque Country. Nevertheless, in Cantabria this augment was only seen when the number of markers was increased from 12 to 23, since the study of 17 Y-STRs was enough to differentiate all haplotypes. Therefore, this study shows that the improvement in forensic parameters by increasing the number of Y-STR markers analyzed is much more pronounced in the case of isolated populations such as the autochthonous population of the Basque Country, as it facilitates the differentiation among similar haplotypes. Moreover, by the use of the PowerPlex(®) Y23 identification of population specific haplotypes increased in both populations. Ultimately, the analysis of 23 Y-STRs differentiated among the two geographically close populations of Basque Country and Cantabria. Indeed it showed significant differences between the Basque Country population and all European populations included, meanwhile Cantabria did exhibit significant proximity with the Iberian and the majority of European populations considered.
Forensic Science International: Genetics Supplement Series, 2008
We present a brief analysis of the advances and perspectives of Forensic Genetics (FG) in a devel... more We present a brief analysis of the advances and perspectives of Forensic Genetics (FG) in a developing country such as ours over the last 10 years, during which time this area of Legal Medicine has been partially consolidated. To speak of FG in our country is to speak of a change in the behaviour of the legal system. Both the criminal prosecution system and the National Legal Medicine System are very recent in Ecuador. The first DNA test was carried out in 1997 for a case of migration in which a paternity test was requested. So far around 5000 paternity tests have been carried out, around 60% in the judicial sphere and 40% privately. Over 200 forensic studies have been carried out in criminal cases since the introduction of the new Criminal Procedure Code a figure which could be insufficient but which, due to the existing legal system, is a significant number. There are currently three unofficial laboratories which carry out forensic studies and the test is now consolidated in court cases. At the same time there has been an evolution in legal regulations with the passing of the recent Criminal Procedure Code, the Childhood and Adolescence Code and the National Legal Medicine System Regulation.
PLoS Genetics, 2013
Numerous studies of human populations in Europe and Asia have revealed a concordance between thei... more Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Ychromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.
Legal Medicine, 2009
Vitreous humour is routinely sampled in Forensic Medicine as several post-mortem analyses can be ... more Vitreous humour is routinely sampled in Forensic Medicine as several post-mortem analyses can be performed. However, it is not used for DNA analyses probably due to its scarce cellularity. In these samples, in which the study of nuclear DNA is difficult, the analysis of mtDNA is an alternative approach. The aim of this study was to investigate the utility of vitreous humour for forensic identification purposes. Samples were collected during vitrectomy from retinopathy patients, in collection bags with saline solution. Blood samples were also obtained in order to contrast results. Before DNA organic extraction, several centrifugation steps were needed to concentrate the vitreous humour samples. Unlike blood, direct amplification of 400-bp fragments of the hipervariable regions I and II (HVI and HVII) was not successful, possibly due to damage to the DNA strand caused by the surgery conditions (UV radiation, oxidative stress). Therefore, amplification of two overlapping fragments for each control region was performed in vitreous humour. In order to eliminate undesired products, all samples were purified by an enzymatic method. Thereafter, mtDNA fragments were sequenced using dye terminators in a MegaBACE 500 capillary sequencer. Sequences of HVI and HVII of approximately 400 bp were obtained from all samples. The sequences obtained from each patient matched almost perfectly those from blood. In summary, herein we describe for the first time a methodology suitable for the mtDNA analysis of vitreous humour samples.
International Journal of Legal Medicine, 2012
This study presents mitochondrial DNA (mtDNA) data from 107 unrelated individuals from two of the... more This study presents mitochondrial DNA (mtDNA) data from 107 unrelated individuals from two of the major ethnic groups in Ecuador: Amerindian Kichwas (n = 65) and Mestizos (n = 42). We characterized the diversity of the matrilineal lineages of these Ecuadorian groups by analyzing the entire mtDNA control region. Different patterns of diversity were observed in the two groups as result of the unique historical and demographic events which have occurred in each population. Higher genetic diversity values were obtained for the Mestizo group than for the Amerindian group. Interestingly, only Native American lineages were detected in the two population samples, but with differences in the haplogroup distribution: Kichwa (A, 49%; B, 3%; C, 8%; and D, 40%) and Mestizo (A, 33%; B, 33%; C, 10%; and D, 24%). Analysis of the complete mtDNA control region proved to be useful to increase the discrimination power between individuals who showed common haplotypes in HVSI and HVSII segments; and added valuable information to the phylogenetic interpretation of mtDNA haplotypes.
Forensic Science International: Genetics, 2014
Forensic Science International: Genetics, 2013
Forensic Science International: Genetics, 2012
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Papers by Carolina Núñez