Publications by authors named "María Victoria Lareu"

34 Publications

Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data.

Front Genet 2020 20;11:581041. Epub 2020 Oct 20.

Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.

The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms and designed for identification purposes. We have broadened reference population data for identification purposes, including data from 240 HGDP-CEPH individuals of native populations from North Africa, the Middle East, Oceania and America. Using the enhanced population data, the panel was evaluated as a marker set for bio-geographical ancestry (BGA) inference, providing a clear differentiation of the five main continental groups of Africa, Europe, East Asia, Native America, and Oceania. An informative degree of differentiation was also achieved for the population variation encompassing North Africa, Middle East, Europe, South Asia, and East Asia. In addition, we explored the potential for individual BGA inference from simple mixed DNA, by simulation of mixed profiles followed by deconvolution of mixture components.
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http://dx.doi.org/10.3389/fgene.2020.581041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7606911PMC
October 2020

Performance of ancestry-informative SNP and microhaplotype markers.

Forensic Sci Int Genet 2019 11 8;43:102141. Epub 2019 Aug 8.

Centre for Forensic Science, School of Mathematical and Physical Sciences (MaPS), Faculty of Science, University of Technology Sydney, Sydney, Australia.

The use of microhaplotypes (MHs) for ancestry inference has added to an increasing number of ancestry-informative markers (AIMs) for forensic application that includes autosomal single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). This study compares bi-allelic and tri-allelic SNPs as well as MH markers for their ability to differentiate African, European, South Asian, East Asian, and American population groups from the 1000 Genomes Phase 3 database. A range of well-established metrics were applied to rank each marker according to the population differentiation potential they measured. These comprised: absolute allele frequency differences (δ); Rosenberg's informativeness for (ancestry) assignment (I); the fixation index (F); and the effective number of alleles (A). A panel consisting of all three marker types resulted in the lowest mean divergence per population per individual (MDPI = 2.16%) when selected by I. However, when marker types were not mixed, MHs were the highest performing markers by most metrics (MDPI < 4%) for differentiation between the five continental populations.
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http://dx.doi.org/10.1016/j.fsigen.2019.102141DOI Listing
November 2019

Global patterns of STR sequence variation: Sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit.

Electrophoresis 2018 11 3;39(21):2708-2724. Epub 2018 Sep 3.

Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.

The 944 individuals of the CEPH human genome diversity panel (HGDP-CEPH), a standard sample set of 51 globally distributed populations, were sequenced using the Illumina ForenSeq™ DNA Signature Prep Kit. The ForenSeq™ system is a single multiplex for the MiSeq/FGx™ massively parallel sequencing instrument, comprising: amelogenin, 27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 SNPforID+Kiddlab autosomal ID-SNPs (plus optionally detected ancestry and phenotyping SNP sets). We report in detail the patterns of sequence variation observed in the repeat regions of the 58 forensic STR loci typed by the ForenSeq™ system. Sequence alleles were characterized and repeat region structures annotated by aligning the ForenSeq™ sequence output to the latest GRCh38 human reference sequence, necessitating the reversal and re-alignment of STR allele sequences reported by the Forenseq™ system in 20 of 58 STRs (plus the reverse alleles in two Y-STRs with duplicated-inverted repeat regions). Individual population sample sizes of the HGDP-CEPH panel do not allow reliable inferences to be made about levels of genetic variability in low frequency STR alleles-where particular sequence variants are found in only a few individuals; but we assessed the occurrence of both population-specific sequence variants and singleton observations; finding each of these in a sizeable proportion of HGDP-CEPH samples, with consequences for planning the co-ordinated compilation of sequence variation on a much larger scale than was required before by forensic laboratories now adopting massively parallel sequencing.
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http://dx.doi.org/10.1002/elps.201800117DOI Listing
November 2018

Ancestry analysis in rural Brazilian populations of African descent.

Forensic Sci Int Genet 2018 09 28;36:160-166. Epub 2018 Jun 28.

Human Genetics Laboratory, Institute of Biological Sciences, University of Brasília, Brazil; Animal Biology Graduate Program, Institute of Biological Sciences, University of Brasília, Brazil. Electronic address:

Rural communities comprise around 20% of Caribbean and South American populations, but are under-represented in autosomal marker databases. That deficiency is problematic for forensic genetics, as it relies on accurate descriptions of genetic variation and population structure. Brazilian populations were shaped by an intense, complex and heterogeneous process of admixture encompassing mainly Amerindians, Sub-Saharan Africans and Europeans. Quilombos are Brazilian populations with significant African descent that have remained genetically isolated to some extent from surrounding populations. In the reported study, we analyzed three rural Quilombo populations: Kalunga; Riacho de Sacutiaba e Sacutiaba; and Mocambo, along with a dataset from the HGDP-CEPH panel. Aiming to contribute to representative genetic databases of forensic interest, we analyse the three rural Quilombos populations and investigate how their genetic makeup relates to their history by analyzing an established forensic test, comprising 46 ancestry-informative (AIM) Indels. The panel was chosen for its high power in differentiating the main contributing populations of Brazil. Parental populations were selected from HGDP-CEPH data available at the forInDel allele frequency browser based on historic patterns applicable to the study populations and the amount of variability observed within and between continents. Our results show the main admixture components in the Quilombos are African and European. Those estimates are in accordance with previous analyses for both uniparental and autosomal markers. PCA, structure analysis and ancestry estimates indicate a correlation between the extent of isolation and the degree of admixture in the Quilombos: Kalunga is the most isolated population and accordingly has a higher African admixture component (67.3%). Sacutiaba is the smallest and most impacted by migration, with the highest European component (46.8%). Mocambo neighbors a Native American population and therefore has the highest Amerindian contribution (12.2%). Our results are consistent with the history and demography of Quilombos. The heterogeneity observed in these populations stresses the genetic diversity that Latin American and Caribbean rural populations can have and reiterates the need to describe them in greater detail.
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http://dx.doi.org/10.1016/j.fsigen.2018.06.018DOI Listing
September 2018

Tracking age-correlated DNA methylation markers in the young.

Forensic Sci Int Genet 2018 09 13;36:50-59. Epub 2018 Jun 13.

Faculty of Mathematics, University of Santiago de Compostela, Spain.

DNA methylation is the most extensively studied epigenetic signature, with a large number of studies reporting age-correlated CpG sites in overlapping genes. However, most of these studies lack sample coverage of individuals under 18 years old and therefore little is known about the progression of DNA methylation patterns in children and adolescents. In the present study we aimed to select candidate age-correlated DNA methylation markers based on public datasets from Illumina BeadChip arrays and previous publications, then to explore the resulting markers in 209 blood samples from donors aged between 2 to 18 years old using the EpiTYPER® DNA methylation analysis system. Results from our analyses identified six genes highly correlated with age in the young, in particular the gene KCNAB3, which indicates its potential as a highly informative and specific age biomarker for childhood and adolescence. We outline a preliminary age prediction model based on quantile regression that uses data from the six CpG sites most strongly correlated with age ranges extended to include children and adolescents.
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http://dx.doi.org/10.1016/j.fsigen.2018.06.011DOI Listing
September 2018

Modified aging of elite athletes revealed by analysis of epigenetic age markers.

Aging (Albany NY) 2018 02;10(2):241-252

Central Forensic Laboratory of the Police, Warsaw, Poland.

Recent progress in epigenomics has led to the development of prediction systems that enable accurate age estimation from DNA methylation data. Our objective was to track responses to intense physical exercise of individual age-correlated DNA methylation markers and to infer their potential impact on the aging processes. The study showed accelerated DNA hypermethylation for two CpG sites in and . Both markers predicted the investigated elite athletes to be several years older than controls and this effect was more substantial in subjects involved in power sports. Accordingly, the complete 5-CpG model revealed age acceleration of elite athletes (=1.503x10) and the result was more significant amongst power athletes (P=1.051x10). The modified methylation of and in top athletes may be accounted for by the biological roles played by these genes. Their known anti-tumour and anti-inflammatory activities suggests that intense physical training has a complex influence on aging and potentially launches signalling networks that contribute to the observed lower risk of elite athletes to develop cardiovascular disease and cancer.
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http://dx.doi.org/10.18632/aging.101385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842850PMC
February 2018

Inference of Ancestry in Forensic Analysis II: Analysis of Genetic Data.

Methods Mol Biol 2016 ;1420:255-85

Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain.

Three approaches applicable to the analysis of forensic ancestry-informative marker data-STRUCTURE, principal component analysis, and the Snipper Bayesian classification system-are reviewed. Detailed step-by-step guidance is provided for adjusting parameter settings in STRUCTURE with particular regard to their effect when differentiating populations. Several enhancements to the Snipper online forensic classification portal are described, highlighting the added functionality they bring to particular aspects of ancestry-informative SNP analysis in a forensic context.
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http://dx.doi.org/10.1007/978-1-4939-3597-0_19DOI Listing
January 2018

Inference of Ancestry in Forensic Analysis I: Autosomal Ancestry-Informative Marker Sets.

Methods Mol Biol 2016 ;1420:233-53

Forensic Genetics Unit, Luis Concheiro Institute of Forensic Sciences, Genomic Medicine Group, University of Santiago de Compostela, Galicia, 15782, Spain.

An expanding choice of ancestry-informative marker single nucleotide polymorphisms (AIM-SNPs) is becoming available for the forensic user in the form of sensitive SNaPshot-based tests or in alternative single-base extension genotyping systems (e.g., Sequenom iPLEX) that can be adapted for analysis with SNaPshot. In addition, alternative ancestry-informative variation: Indels and STRs can be analyzed using direct PCR-to-CE techniques that offer the possibility to detect mixed profiles. We review the current forensically viable AIM panels, their optimized PCR multiplexes, and the population differentiation power they offer. We also describe how improved population divergence balance can be achieved with the enlarged multiplex scales of next-generation sequencing approaches to enable analysis of admixed individuals without biased estimation of co-ancestry proportions.
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http://dx.doi.org/10.1007/978-1-4939-3597-0_18DOI Listing
January 2018

SNP Markers as Additional Information to Resolve Complex Kinship Cases.

Transfus Med Hemother 2015 Nov 4;42(6):385-8. Epub 2015 Nov 4.

Molecular Oncology, Portuguese Institute of Oncology, Porto, Portugal; ICBAS, Abel Salazar Institute for the Biomedical Sciences, University of Porto, Porto, Portugal;  LPCC, Research Department-Portuguese League Against Cancer (NRNorte), Porto, Portugal.

Background: DNA profiling with sets of highly polymorphic autosomal short tandem repeat (STR) markers has been applied in various aspects of human identification in forensic casework for nearly 20 years. However, in some cases of complex kinship investigation, the information provided by the conventionally used STR markers is not enough, often resulting in low likelihood ratio (LR) calculations. In these cases, it becomes necessary to increment the number of loci under analysis to reach adequate LRs. Recently, it has been proposed that single nucleotide polymorphisms (SNPs) could be used as a supportive tool to STR typing, eventually even replacing the methods/markers now employed.

Methods: In this work, we describe the results obtained in 7 revised complex paternity cases when applying a battery of STRs, as well as 52 human identification SNPs (SNPforID 52plex identification panel) using a SNaPshot methodology followed by capillary electrophoresis.

Results: Our results show that the analysis of SNPs, as complement to STR typing in forensic casework applications, would at least increase by a factor of 4 total PI values and correspondent Essen-Möller's W value.

Conclusions: We demonstrated that SNP genotyping could be a key complement to STR information in challenging casework of disputed paternity, such as close relative individualization or complex pedigrees subject to endogamous relations.
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http://dx.doi.org/10.1159/000440832DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4698646PMC
November 2015

Completion of a worldwide reference panel of samples for an ancestry informative Indel assay.

Forensic Sci Int Genet 2015 Jul 25;17:75-80. Epub 2015 Mar 25.

Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Spain.

The use of ancestry informative markers (AIMs) in forensic analysis is of considerable utility since ancestry inference can progress an investigation when no identification has been made of DNA from the crime-scene. Short-amplicon markers, including insertion deletion polymorphisms, are particularly useful in forensic analysis due to their mutational stability, capacity to amplify degraded samples and straightforward amplification technique. In this study we report the completion of H952 HGDP-CEPH panel genotyping with a set of 46 AIM-Indels. The study adds Central South Asian and Middle Eastern population data, allowing a comparison of patterns of variation in Eurasia for these markers, in order to enhance their use in forensic analyses, particularly when combined with sets of ancestry informative SNPs. Ancestry analysis using principal component analysis and Bayesian methods indicates that a proportion of classification error occurs with European-Middle East population comparisons, but the 46 AIM-Indels have the capability to differentiate six major population groups when European-Central South Asian comparisons are made. These findings have relevance for forensic ancestry analyses in countries where South Asians form much of the demographic profile, including the UK, USA and South Africa. A novel third allele detected in MID-548 was characterized - despite a low frequency in the HGDP-CEPH panel samples, it appears confined to Central South Asian populations, increasing the ability to differentiate this population group. The H952 data set was implemented in a new open access SPSmart frequency browser - forInDel: Forensic Indel browser.
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http://dx.doi.org/10.1016/j.fsigen.2015.03.011DOI Listing
July 2015

"New turns from old STaRs": enhancing the capabilities of forensic short tandem repeat analysis.

Electrophoresis 2014 Nov 16;35(21-22):3173-87. Epub 2014 Jul 16.

Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.

The field of research and development of forensic STR genotyping remains active, innovative, and focused on continuous improvements. A series of recent developments including the introduction of a sixth dye have brought expanded STR multiplex sizes while maintaining sensitivity to typical forensic DNA. New supplementary kits complimenting the core STRs have also helped improve analysis of challenging identification cases such as distant pairwise relationships in deficient pedigrees. This article gives an overview of several recent key developments in forensic STR analysis: availability of expanded core STR kits and supplementary STRs, short-amplicon mini-STRs offering practical options for highly degraded DNA, Y-STR enhancements made from the identification of rapidly mutating loci, and enhanced analysis of genetic ancestry by analyzing 32-STR profiles with a Bayesian forensic classifier originally developed for SNP population data. As well as providing scope for genotyping larger numbers of STRs optimized for forensic applications, the launch of compact next-generation sequencing systems provides considerable potential for genotyping the sizeable proportion of nucleotide variation existing in forensic STRs, which currently escapes detection with CE.
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http://dx.doi.org/10.1002/elps.201400095DOI Listing
November 2014

Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing.

Electrophoresis 2013 Apr 18;34(8):1151-62. Epub 2013 Mar 18.

Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain.

There is growing interest in developing additional DNA typing techniques to provide better investigative leads in forensic analysis. These include inference of genetic ancestry and prediction of common physical characteristics of DNA donors. To date, forensic ancestry analysis has centered on population-divergent SNPs but these binary loci cannot reliably detect DNA mixtures, common in forensic samples. Furthermore, STR genotypes, forming the principal DNA profiling system, are not routinely combined with forensic SNPs to strengthen frequency data available for ancestry inference. We report development of a 12-STR multiplex composed of ancestry informative marker STRs (AIM-STRs) selected from 434 tetranucleotide repeat loci. We adapted our online Bayesian classifier for AIM-SNPs: Snipper, to handle multiallele STR data using frequency-based training sets. We assessed the ability of the 12-plex AIM-STRs to differentiate CEPH Human Genome Diversity Panel populations, plus their informativeness combined with established forensic STRs and AIM-SNPs. We found combining STRs and SNPs improves the success rate of ancestry assignments while providing a reliable mixture detection system lacking from SNP analysis alone. As the 12 STRs generally show a broad range of alleles in all populations, they provide highly informative supplementary STRs for extended relationship testing and identification of missing persons with incomplete reference pedigrees. Lastly, mixed marker approaches (combining STRs with binary loci) for simple ancestry inference tests beyond forensic analysis bring advantages and we discuss the genotyping options available.
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http://dx.doi.org/10.1002/elps.201200621DOI Listing
April 2013

SNPs as Supplements in Simple Kinship Analysis or as Core Markers in Distant Pairwise Relationship Tests: When Do SNPs Add Value or Replace Well-Established and Powerful STR Tests?

Transfus Med Hemother 2012 Jun 12;39(3):202-210. Epub 2012 May 12.

Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Galicia, Spain.

BACKGROUND: Genetic tests for kinship testing routinely reach likelihoods that provide virtual proof of the claimed relationship by typing microsatellites-commonly consisting of 12-15 standard forensic short tandem repeats (STRs). Single nucleotide polymorphisms (SNPs) have also been applied to kinship testing but these binary markers are required in greater numbers than multiple-allele STRs. However SNPs offer certain advantageous characteristics not found in STRs, including, much higher mutational stability, good performance typing highly degraded DNA, and the ability to be readily up-scaled to very high marker numbers reaching over a million loci. This article outlines kinship testing applications where SNPs markedly improve the genetic data obtained. In particular we explore the minimum number of SNPs that will be required to confirm pairwise relationship claims in deficient pedigrees that typify missing persons' identification or war grave investigations where commonly few surviving relatives are available for comparison and the DNA is highly degraded. METHODS: We describe the application of SNPs alongside STRs when incomplete profiles or allelic instability in STRs create ambiguous results, we review the use of high density SNP arrays when the relationship claim is very distant, and we outline simulations of kinship analyses with STRs supplemented with SNPs in order to estimate the practical limit of pairwise relationships that can be differentiated from random unrelated pairs from the same population. RESULTS: The minimum number of SNPs for robust statistical inference of parent-offspring relationships through to those of second cousins (S-3-3) is estimated for both simple, single multiplex SNP sets and for subsets of million-SNP arrays. CONCLUSIONS: There is considerable scope for resolving ambiguous STR results and for improving the statistical power of kinship analysis by adding small-scale SNP sets but where the pedigree is deficient the pairwise relationships must be relatively close. For more distant relationships it is possible to reduce chip-based SNP arrays from the million+ markers down to ∼7,000. However, such numbers indicate that current genotyping approaches will not be able to deliver sufficient data to resolve distant pairwise relationships from the limited DNA typical of the most challenging identification cases.
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http://dx.doi.org/10.1159/000338857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375139PMC
June 2012

Differentiation of African components of ancestry to stratify groups in a case-control study of a Brazilian urban population.

Genet Test Mol Biomarkers 2012 Jun 30;16(6):524-30. Epub 2012 Jan 30.

Faculty of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil.

Background: Balancing the subject composition of case and control groups to create homogenous ancestries between each group is essential for medical association studies.

Methods: We explored the applicability of single-tube 34-plex ancestry informative markers (AIM) single nucleotide polymorphisms (SNPs) to estimate the African Component of Ancestry (ACA) to design a future case-control association study of a Brazilian urban sample.

Results: One hundred eighty individuals (107 case group; 73 control group) self-described as white, brown-intermediate or black were selected. The proportions of the relative contribution of a variable number of ancestral population components were similar between case and control groups. Moreover, the case and control groups demonstrated similar distributions for ACA <0.25 and >0.50 categories. Notably a high number of outlier values (23 samples) were observed among individuals with ACA <0.25. These individuals presented a high probability of Native American and East Asian ancestral components; however, no individuals originally giving these self-described ancestries were observed in this study.

Conclusions: The strategy proposed for the assessment of ancestry and adjustment of case and control groups for an association study is an important step for the proper construction of the study, particularly when subjects are taken from a complex urban population. This can be achieved using a straight forward multiplexed AIM-SNPs assay of highly discriminatory ancestry markers.
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http://dx.doi.org/10.1089/gtmb.2011.0267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378015PMC
June 2012

Mitochondrial echoes of first settlement and genetic continuity in El Salvador.

PLoS One 2009 Sep 2;4(9):e6882. Epub 2009 Sep 2.

Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.

Background: From Paleo-Indian times to recent historical episodes, the Mesoamerican isthmus played an important role in the distribution and patterns of variability all around the double American continent. However, the amount of genetic information currently available on Central American continental populations is very scarce. In order to shed light on the role of Mesoamerica in the peopling of the New World, the present study focuses on the analysis of the mtDNA variation in a population sample from El Salvador.

Methodology/principal Findings: We have carried out DNA sequencing of the entire control region of the mitochondrial DNA (mtDNA) genome in 90 individuals from El Salvador. We have also compiled more than 3,985 control region profiles from the public domain and the literature in order to carry out inter-population comparisons. The results reveal a predominant Native American component in this region: by far, the most prevalent mtDNA haplogroup in this country (at approximately 90%) is A2, in contrast with other North, Meso- and South American populations. Haplogroup A2 shows a star-like phylogeny and is very diverse with a substantial proportion of mtDNAs (45%; sequence range 16090-16365) still unobserved in other American populations. Two different Bayesian approaches used to estimate admixture proportions in El Salvador shows that the majority of the mtDNAs observed come from North America. A preliminary founder analysis indicates that the settlement of El Salvador occurred about 13,400+/-5,200 Y.B.P.. The founder age of A2 in El Salvador is close to the overall age of A2 in America, which suggests that the colonization of this region occurred within a few thousand years of the initial expansion into the Americas.

Conclusions/significance: As a whole, the results are compatible with the hypothesis that today's A2 variability in El Salvador represents to a large extent the indigenous component of the region. Concordant with this hypothesis is also the observation of a very limited contribution from European and African women ( approximately 5%). This implies that the Atlantic slave trade had a very small demographic impact in El Salvador in contrast to its transformation of the gene pool in neighbouring populations from the Caribbean facade.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006882PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731219PMC
September 2009

Ancestry analysis in the 11-M Madrid bomb attack investigation.

PLoS One 2009 Aug 11;4(8):e6583. Epub 2009 Aug 11.

Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain.

The 11-M Madrid commuter train bombings of 2004 constituted the second biggest terrorist attack to occur in Europe after Lockerbie, while the subsequent investigation became the most complex and wide-ranging forensic case in Spain. Standard short tandem repeat (STR) profiling of 600 exhibits left certain key incriminatory samples unmatched to any of the apprehended suspects. A judicial order to perform analyses of unmatched samples to differentiate European and North African ancestry became a critical part of the investigation and was instigated to help refine the search for further suspects. Although mitochondrial DNA (mtDNA) and Y-chromosome markers routinely demonstrate informative geographic differentiation, the populations compared in this analysis were known to show a proportion of shared mtDNA and Y haplotypes as a result of recent gene-flow across the western Mediterranean, while any two loci can be unrepresentative of the ancestry of an individual as a whole. We based our principal analysis on a validated 34plex autosomal ancestry-informative-marker single nucleotide polymorphism (AIM-SNP) assay to make an assignment of ancestry for DNA from seven unmatched case samples including a handprint from a bag containing undetonated explosives together with personal items recovered from various locations in Madrid associated with the suspects. To assess marker informativeness before genotyping, we predicted the probable classification success for the 34plex assay with standard error estimators for a naïve Bayesian classifier using Moroccan and Spanish training sets (each n = 48). Once misclassification error was found to be sufficiently low, genotyping yielded seven near-complete profiles (33 of 34 AIM-SNPs) that in four cases gave probabilities providing a clear assignment of ancestry. One of the suspects predicted to be North African by AIM-SNP analysis of DNA from a toothbrush was identified late in the investigation as Algerian in origin. The results achieved illustrate the benefit of adding specialized marker sets to provide enhanced scope and power to an already highly effective system of DNA analysis for forensic identification.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0006583PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719087PMC
August 2009

Population data on 15 autosomal STRs in a sample from Colombia.

Forensic Sci Int Genet 2009 Jun 13;3(3):e81-2. Epub 2008 Sep 13.

Institute of Legal Medicine, Genomics Medicine Group, University of Santiago de Compostela, Spain.

We present population genetic data of 15 STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, PENTA D, PENTA E, TH01, TPOX and VWA) obtained from a sample of 617 unrelated individuals from Colombia. Deviations from Hardy-Weinberg equilibrium were assessed and allele frequencies and parameters of forensic interest for each STR were calculated. The combined power of exclusion (PE) and the combined power of discrimination (PD) for the 15 tested STR loci were 0, 99999895 and more than 0, 9999999, respectively. The combined MP value was 1 in 1, 07888 x 10(-17). Population comparisons between our sample and neighbouring populations from Latin America were carried out. Significant differences in above six markers were observed between our sample and two populations from Rio de Janeiro.
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http://dx.doi.org/10.1016/j.fsigen.2008.08.002DOI Listing
June 2009

New population and phylogenetic features of the internal variation within mitochondrial DNA macro-haplogroup R0.

PLoS One 2009 2;4(4):e5112. Epub 2009 Apr 2.

Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.

Background: R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (approximately 40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies.

Methodology/principal Findings: We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (approximately 57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6+/-8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM).

Conclusions/significance: In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005112PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2660437PMC
July 2009

The genetic male component of two South-Western Colombian populations.

Forensic Sci Int Genet 2009 Mar 8;3(2):e59-61. Epub 2008 Aug 8.

Pediatrics Department, College of Medicine, University of Cauca, Popayán, Colombia.

In the recent history of Colombia, two factors have contributed to change the population structure, the Spanish conquest and the slave trading promoted principally by Portugal, England and Spain. As a consequence the native population of Colombia has been reduced and mixed with the European and African arriving groups. To assess the male ancestry of the Cauca population, we have examined the frequency of the major Y-chromosome lineages by typing 30 Y-SNPs in two populations from this region: 105 Afro-Colombian individuals and 110 Caucasian-Mestizo individuals. Among the 33 haplogroups defined with the SNPs analysed, 15 haplogroups were detected, 10 of them being shared by both populations. In order to investigate how the level of admixture is, and to compare the genetic background with other neighbour populations, other South American samples previously published were used for comparative analysis.
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http://dx.doi.org/10.1016/j.fsigen.2008.06.006DOI Listing
March 2009

Finding genes that underlie physical traits of forensic interest using genetic tools.

Forensic Sci Int Genet 2007 Jun 23;1(2):100-4. Epub 2007 Mar 23.

Institute of Legal Medicine, University of Santiago de Compostela, Spain.

Association studies using SNPs provides one of the best tools that we have at the moment for looking for genes involved in physical traits. However the studies should be carefully designed from the very beginning in all the steps of the procedure: pre-genotyping, genotyping and the mathematical analysis of the results. If the actual knowledge is correctly applied in the design of the study the probability of being successful in finding an association can be considerably increased. Improved statistical analysis techniques are helping in the robustness of the findings. The current consensus from the literature indicates that this would be a good time to investigate complex or quantitative traits via dense SNP genotyping, and a number of studies have been published, providing potential models. The state of the art of candidate genes for pigmentation, stature and facial morphology is described.
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http://dx.doi.org/10.1016/j.fsigen.2007.02.009DOI Listing
June 2007

Shipwrecks and founder effects: divergent demographic histories reflected in Caribbean mtDNA.

Am J Phys Anthropol 2005 Dec;128(4):855-60

Unidad de Genética, Instituto de Medicina Legal, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain.

During the period of the Atlantic slave trade (15th-19th centuries), millions of people were forced to move from Africa to many American destinations, changing dramatically the human landscape of the Americas. Here, we analyze mitochondrial DNA from two different American populations with African ancestry, with hitherto unknown European and Native American components. On the basis of historical records, African-Americans from Chocó (Colombia) and the Garífunas (or "Black Carib") of Honduras are likely to have had very different demographic histories, with a significant founder effect in the formation of the latter. Both the common features and differences are reflected in their mtDNA composition. Both show a minor component (approximately 16%) from Native Central/South Americans and a larger component (approximately 84%) from sub-Saharan Africans. The latter component is very diverse in the African-Americans from Chocó, similar to that of sub-Saharan Africans, but much less so in the Garífunas, with several mtDNA types elevated to high frequency, suggesting the action of genetic drift.
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http://dx.doi.org/10.1002/ajpa.20117DOI Listing
December 2005

Autosomal microsatellite data from Northwestern Colombia.

Forensic Sci Int 2006 Jul 15;160(2-3):217-20. Epub 2005 Jul 15.

Institute of Biology, Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia.

Allele frequencies and some forensic parameters for 12 autosomal microsatellites (CSF1PO, TPOX, THO1, VWA, D16S539, D7S820, D13S317, D5S818, F13A1, FESFPS, F13B, LPL) were estimated from three departments from Northwestern Colombia. The total number of samples analysed was 1045 individuals. Comparative analysis among the three studied departments and with other published Colombian populations were also performed and discussed.
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http://dx.doi.org/10.1016/j.forsciint.2005.05.034DOI Listing
July 2006

Genotyping SNPs with the LightCycler.

Methods Mol Biol 2005 ;297:127-40

Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain.

Here, a single nucleotide polymorphism typing methodology is described based on polymerase chain reaction monitoring, in real time, of fluorescently labeled amplified products using the LightCycler. The main advantages of the system are the time required for the analysis (about 20 min), combined with the robustness, accuracy, and the sensitivity of the method.
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http://dx.doi.org/10.1385/1-59259-867-6:127DOI Listing
April 2005

Y-chromosome STR-haplotype typing in El Salvador.

Forensic Sci Int 2004 May;142(1):45-9

Facultad de Medicina, Instituto de Medicina Legal, University of Santiago de Compostela, C/San Francisco s/n, 15782 Santiago de Compostela, Galicia, Spain.

Eight Y-chromosome STRs were investigated in a male population sample from El Salvador. Complete Y-chromosomal STRs haplotypes were obtained in 121 individuals, among which 107 different haplotypes were observed. The two most common haplotypes were shared by approximately 4% of the sample, while 100 haplotypes were unique. The gene diversity was 0.9883 and the discrimination capacity was 0.8926. The combined Y-chromosome STR polymorphisms provide a powerful discrimination tool for routine forensic applications.
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http://dx.doi.org/10.1016/j.forsciint.2004.02.004DOI Listing
May 2004

The African diaspora: mitochondrial DNA and the Atlantic slave trade.

Am J Hum Genet 2004 Mar 10;74(3):454-65. Epub 2004 Feb 10.

Unidad de Genética Forense, Instituto de Medicina Legal, Universidad de Santiago de Compostela, Galicia, Spain.

Between the 15th and 19th centuries ad, the Atlantic slave trade resulted in the forced movement of approximately 13 million people from Africa, mainly to the Americas. Only approximately 11 million survived the passage, and many more died in the early years of captivity. We have studied 481 mitochondrial DNAs (mtDNAs) of recent African ancestry in the Americas and in Eurasia, in an attempt to trace them back to particular regions of Africa. Our results show that mtDNAs in America and Eurasia can, in many cases, be traced to broad geographical regions within Africa, largely in accordance with historical evidence, and raise the possibility that a greater resolution may be possible in the future. However, they also indicate that, at least for the moment, considerable caution is warranted when assessing claims to be able to trace the ancestry of particular lineages to a particular locality within modern-day Africa.
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http://dx.doi.org/10.1086/382194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182259PMC
March 2004

Nine autosomal STRs genotype profiles in a sample from Córdoba (Argentina).

Forensic Sci Int 2004 Jan;139(1):81-3

Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, C/San Francisco s/n, 15782, Santiago de Compostela, Spain.

Nine STRs loci have been typed in a sample from Córdoba (Argentina).
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http://dx.doi.org/10.1016/j.forsciint.2003.07.005DOI Listing
January 2004

Y-chromosome STR haplotypes in Córdoba (Argentina).

Forensic Sci Int 2003 Nov;137(2-3):217-20

Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, C/San Francisco s/n, 15782 Santiago de Compostela, Spain.

Eight Y-chromosome STRs were investigated in a male population sample from Córdoba region (Argentina). Complete Y-chromosomal STRs haplotypes were obtained in 100 individuals, among which 91 different haplotypes were observed. The most common haplotype was shared by 4% of the sample, while 86 haplotypes were unique. The gene diversity was 0.9875 and the discrimination capacity was 0.8600. The combined polymorphism provides a powerful discrimination tool for routine forensic applications.
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http://dx.doi.org/10.1016/j.forsciint.2003.07.006DOI Listing
November 2003

STR-CODIS typing in Greece.

Forensic Sci Int 2003 Oct;137(1):104-6

DNA Analysis Laboratory, Legal Medicine Department of Athens, 10 Anapafseos Street, Athens 11636, Spain.

Thirteen STRs loci have been typed in a sample from Greece.
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http://dx.doi.org/10.1016/s0379-0738(03)00298-6DOI Listing
October 2003

The making of the African mtDNA landscape.

Am J Hum Genet 2002 Nov 22;71(5):1082-111. Epub 2002 Oct 22.

Unidad de Genética Forense, Universidad de Santiago de Compostela, Santiago de Compostela, Galicia, Spain.

Africa presents the most complex genetic picture of any continent, with a time depth for mitochondrial DNA (mtDNA) lineages >100,000 years. The most recent widespread demographic shift within the continent was most probably the Bantu dispersals, which archaeological and linguistic evidence suggest originated in West Africa 3,000-4,000 years ago, spreading both east and south. Here, we have carried out a thorough phylogeographic analysis of mtDNA variation in a total of 2,847 samples from throughout the continent, including 307 new sequences from southeast African Bantu speakers. The results suggest that the southeast Bantu speakers have a composite origin on the maternal line of descent, with approximately 44% of lineages deriving from West Africa, approximately 21% from either West or Central Africa, approximately 30% from East Africa, and approximately 5% from southern African Khoisan-speaking groups. The ages of the major founder types of both West and East African origin are consistent with the likely timing of Bantu dispersals, with those from the west somewhat predating those from the east. Despite this composite picture, the southeastern African Bantu groups are indistinguishable from each other with respect to their mtDNA, suggesting that they either had a common origin at the point of entry into southeastern Africa or have undergone very extensive gene flow since.
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http://dx.doi.org/10.1086/344348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC385086PMC
November 2002