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P Gill, L Gusmão,
H Haned,
W R Mayr,
N Morling,
W Parson,
L Prieto,
M Prinz,
H Schneider,
P M Schneider,
B S Weir
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ABSTRACT: DNA profiling of biological material from scenes of crimes is often complicated because the amount of DNA is limited and the quality of the DNA may be compromised. Furthermore, the sensitivity of STR typing kits has been continuously improved to detect low level DNA traces. This may lead to (1) partial DNA profiles and (2) detection of additional alleles. There are two key phenomena to consider: allelic or locus 'drop-out', i.e. 'missing' alleles at one or more genetic loci, while 'drop-in' may explain alleles in the DNA profile that are additional to the assumed main contributor(s). The drop-in phenomenon is restricted to 1 or 2 alleles per profile. If multiple alleles are observed at more than two loci then these are considered as alleles from an extra contributor and analysis can proceed as a mixture of two or more contributors. Here, we give recommendations on how to estimate probabilities considering drop-out, Pr(D), and drop-in, Pr(C). For reasons of clarity, we have deliberately restricted the current recommendations considering drop-out and/or drop-in at only one locus. Furthermore, we offer recommendations on how to use Pr(D) and Pr(C) with the likelihood ratio principles that are generally recommended by the International Society of Forensic Genetics (ISFG) as measure of the weight of the evidence in forensic genetics. Examples of calculations are included. An Excel spreadsheet is provided so that scientists and laboratories may explore the models and input their own data.
Forensic science international. Genetics 08/2012; 6(6):679-88. · 2.42 Impact Factor
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ABSTRACT: Improving the amplification and analysis of highly degraded DNA extracts has been a longstanding area of research in forensic genetics. One of the most promising recent developments in analysis of degraded DNA is the availability of short, biallelic insertion-deletion length polymorphisms (InDels) in highly multiplexed assays. InDels share many of the favourable characteristics of single-nucleotide polymorphisms (SNPs) that make them ideal markers for analysis of degraded DNA, including: analysis in short amplicon size ranges, high multiplexing capability and low mutation rates. In addition, as length-based polymorphisms, InDels can be analysed with the same simple dye-labelled PCR primer methods as standard forensic short tandem repeats. Separation and detection of fluorescently dye-labelled PCR products by capillary electrophoresis eliminate the multiple step protocols required by SNP typing with single-base extension assays and provide a closer relationship between the input DNA and the profile peak height ratios. Therefore InDel genotyping represents an effective new approach for human identification that adds informative new loci to the existing battery of forensic markers. To assess the utility of InDels for forensic analysis, we characterised population variation with two InDel identification assays: the 30-plex Qiagen DIPplex panel and a 38-plex panel developed by Pereira et al. in 2009. Allele frequencies were generated for the 68 markers in US African American, Caucasian, East Asian and Hispanic samples. We made a thorough assessment of the individual and combined performance of the InDel sets, as well as characterising profile artifacts and other issues related to the routine use of these newly developed forensic assays based on artificially degraded DNA and mixed source samples.
Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 06/2012; 126(5):725-37. · 2.59 Impact Factor
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P. Brito,
M. Carvalho,
V. Gomes,
M.M. Melo,
V. Bogas,
F. Balsa,
L. Andrade,
A. Serra,
V. Lopes, L. Gusmão,
M.J. Anjos,
F. Corte-Real
Forensic Science International: Genetics Supplement Series. 12/2011; 3:e369-e370.
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ABSTRACT: The occurrence of Mendelian incompatibilities between true father and child is not an uncommon situation. Thus, in paternity investigations, when only a few are observed, it is possible that the alleged father is either the real father or his close relative. In this study, we intended to test how a set of autosomal indels can complement the results obtained with a routine battery of STRs in paternity investigations where the alleged father is, in fact, a close relative of the real one. We analyzed 100 uncle/nephew and grandfather/grandchild unrelated duos, through the amplification of 15 STR markers and a set of 38 non-coding bi-allelic indels. For each duo, we determined the number of observed incompatibilities and calculated the LR assuming a father/son relationship, for both STRs and indels. As expected, in a significant proportion of cases, no incompatibilities were found. In these instances, indel's LR contribution was always in favour of the “wrong” hypothesis, strengthening a false paternity
Forensic Science International Genetics Supplement Series 12/2011; 3(1):e9-e10.
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ABSTRACT: In this work we aimed to evaluate the African, European and Native American ancestral contributions to different Argentinean populations. A set of 46 ancestry-informative insertion–deletion polymorphisms (AIM-Indels) was used to type 279 unrelated individuals from urban populations of six provinces located in distant geographical regions of Argentina. The STRUCTURE analysis showed that the African contribution presented the lowest values, with no significant differences among the studied regions (between 2 and 3%). As expected, the population from Buenos Aires appeared to have the highest European ancestry contribution (86.8%). In contrast, the Native American component is better represented in urban samples from the northern and southern regions of the country, reaching almost 40% in both Tucuman and Santa Cruz. These differences are also revealed by the Fst analysis results, where most of the significant genetic distances are between Buenos Aires and the other populations. The results are in agreem
Forensic Science International Genetics Supplement Series 12/2011; 3(1):e387-e388.
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M Carvalho,
P Brito,
A M Bento,
V Gomes,
H Antunes,
H Afonso Costa,
V Lopes,
A Serra,
F Balsa,
L Andrade,
M J Anjos,
F Corte-Real, L Gusmão
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ABSTRACT: The aim of the present work was to study the origin of paternal and maternal lineages in Guinea-Bissau population, inferred by phylogeographic analyses of mtDNA and Y chromosome defined haplogroups. To determine the male lineages present in Guinea-Bissau, 33 unrelated males were typed using a PCR-SNaPshot multiplex based method including 24 Y-SNPs, which characterize the main haplogroups in sub-Saharan Africa and Western Europe. In the same samples, 17 Y-STRs (included in the YFiler kit, Applied Biosystems) were additionally typed. The most frequent lineages observed were E1b1a (xE1b1a4,7)-M2 (68%) and E1a-M33 (15%). The European haplogroup R1b1-P25 was represented with a frequency of 12%. The two hypervariable mtDNA regions were sequenced in 79 unrelated individuals from Guinea-Bissau, and haplogroups were classified based on control region motifs using mtDNA manager. A high diversity of haplogroups was determined in our sample being the most frequent haplogroups characteristic of populations from sub-Saharan Africa, namely L2a1 (15%), L3d (13%), L2c (9%), L3e4 (9%), L0a1 (8%), L1b (6%) and L1c1 (6%). None of the typical European haplogroups (H, J and T) were found in the present sample of Guinea-Bissau. From our results, it is possible to confirm that Guinea-Bissau presents a typically West African profile, marked by a high frequency of the Y chromosome haplogroup E1b1a(xE1b1a4,7)-M2 and a high proportion of mtDNA lineages belonging to the sub-Saharan specific sub-clusters L1 to L3 (89%). A small European influx has been also detected, although restricted to the male lineages.
Forensic science international. Genetics 11/2010; 5(2):114-6. · 2.42 Impact Factor
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ABSTRACT: The use of non-human DNA typing in forensic science investigations, and specifically that from animal DNA, is ever increasing. The term animal DNA in this document refers to animal species encountered in a forensic science examination but does not include human DNA. Non-human DNA may either be: the trade and possession of a species, or products derived from a species, which is contrary to legislation; as evidence where the crime is against a person or property; instances of animal cruelty; or where the animal is the offender. The first instance is addressed by determining the species present, and the other scenarios can often be addressed by assigning a DNA sample to a particular individual organism. Currently there is little standardization of methodologies used in the forensic analysis of animal DNA or in reporting styles. The recommendations in this document relate specifically to animal DNA that is integral to a forensic science investigation and are not relevant to the breeding of animals for commercial purposes. This DNA commission was formed out of discussions at the International Society for Forensic Genetics 23rd Congress in Buenos Aires to outline recommendations on the use of non-human DNA in a forensic science investigation. Due to the scope of non-human DNA typing that is possible, the remit of this commission is confined to animal DNA typing only.
Forensic science international. Genetics 11/2010; 5(5):501-5. · 2.42 Impact Factor
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ABSTRACT: The male-mediated genetic legacy of the Pyrenean population was assessed through the analysis of 12 Y-STR and 27 Y-SNP loci in a sample of 169 males from 5 main geographical areas in the Spanish Pyrenees: Cinco Villas (Western Pyrenees), Jacetania and Valle de Arán (Central Pyrenees) and Alto Urgel and Cerdaña (Eastern Pyrenees). In the Iberian context, the Pyrenean samples present some specificities, being characterizeded by a high proportion of chromosomes R1b1b2-M269 (including the usually uncommon R1b1b2d-SRY(2627) and R1b1b2c-M153 types) or I2a2-M26 and low proportions of other haplogroups. Our results indicate that an old pre-Neolithic substrate is preponderant in populations of the whole Pyrenean fringe. However, AMOVA revealed a high level of substructure within Pyrenean populations, partially explained by drift effects as well as by the signature of an ancient genetic differentiation between Western and Eastern Pyrenees.
Annals of Human Genetics 10/2008; 73(1):42-53. · 2.57 Impact Factor
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ABSTRACT: For the Portuguese population no data were previously available for autosomal SNP genetic diversity and population structure. In this work we characterized 52 autosomal SNPs in the three regions from continental Portugal (North, Centre and South) using the SNPforID multiplex assay. Comparisons made between the three regions revealed genetic homogeneity of the studied SNPs throughout the country, allowing the use of a common database. Allele frequencies are presented for all markers as well as observed heterozygosity, discrimination power and genetic distances (FST) between regions. No significant deviations from Hardy–Weinberg equilibrium were detected. The high power of discrimination obtained in the Portuguese population confirms the utility of the 52-plex in identification studies.
Forensic Science International Genetics Supplement Series 08/2008; 1(1):358-360.
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ABSTRACT: Population data regarding autosomal single nucleotide polymorphisms (SNPs) variation in African populations are very limited. The aim of this work was to provide enhanced sampling and a more representative coverage of the African continent. We studied two sub-Saharan African populations (Uganda and Angola) using the SNPforID 52-plex assay. Allele frequencies, observed heterozygosity, discrimination power and genetic distance (FST) between populations are reported for all markers. Comparisons revealed a low but significant genetic distance between the two populations. No significant deviations from Hardy–Weinberg equilibrium or associations between loci were detected. The forensic efficiency parameters highlight the potential of the SNPforID multiplex for identification purposes also in African populations.
Forensic Science International Genetics Supplement Series 08/2008; 1(1):361-363.
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ABSTRACT: The European Gypsies, commonly referred to as Roma, are represented by a vast number of groups spread across many countries. Although sharing a common origin, the Gypsy groups are highly heterogeneous as a consequence of genetic drift and different levels of admixture with surrounding populations. With this study we aimed at contributing to the knowledge of the Roma history by studying 17 Y-STR and 34 Y-SNP loci in a sample of 126 Portuguese Gypsies. Distinct genetic hallmarks of their past and migration route were detected, namely: an ancestral component, shared by all Roma groups, that reflects their origin in India (H1a-M82; approximately 17%); an influence from their long permanence in the Balkans/Middle-East region (J2a1b-M67, J2a1b1-M92, I-M170, Q-M242; approximately 31%); traces of contacts with European populations preceding the entrance in the Iberian Peninsula (R1b1c-M269, J2b1a-M241; approximately 10%); and a high proportion of admixture with the non-Gypsy population from Iberia (R1b1c-M269, R1-M173/del.M269, J2a-M410, I1b1b-M26, E3b1b-M81; approximately 37%). Among the Portuguese Gypsies the proportion of introgression from host populations is higher than observed in other groups, a fact which is somewhat unexpected since the arrival of the Roma to Portugal is documented to be more recent than in Central or East Europe.
Annals of Human Genetics 04/2008; 72(Pt 2):215-27. · 2.57 Impact Factor
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ABSTRACT: In this work, we present population genetic data of 10 X-chromosome STRs (DXS8378, DXS9898, DXS8377, HPRTB, GATA172D05, DXS7423, DXS6809, DXS7132, DXS101 and DXS6789) obtained from sample of 145 unrelated female individuals belonging to Valencia (Spain), a region located in the east of the Iberian Peninsula. All the markers studied present high genetic diversities, similar to those previously reported in other European population samples. No deviations from Hardy-Weinberg equilibrium were observed, with the exception of DXS101 locus. Allele frequencies and parameters of forensic interest for each X-STR were calculated. High mean exclusion chance and power of discrimination values were obtained by combining these 10 X-linked markers. Population comparisons (exact test of population differentiation; pairwise genetic distances) were carried out and low genetic distances were found between our sample and those from other Spanish or European regions.
Forensic science international 01/2008; 173(2-3):193-6. · 2.10 Impact Factor
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ABSTRACT: Twenty biallelic Y chromosome markers were analyzed in Angolares, Forros and Tongas, three population groups from the African archipelago of São Tomé e Príncipe. While most male lineages belonged to sub-Saharan haplogroups, the component of European origin added up 23.9% in the archipelago. This contrasts with the reported absence of European mtDNA lineages, and the combined findings testify to a strong sex-biased admixture process during the long-lasting colonial period in São Tomé e Príncipe. Furthermore, the male mediated European component was clearly found to be out of proportion to the small demographic impact of the Portuguese on the islands, reflecting high variance in the reproductive success of the individuals that contributed to its peopling. The male portion of European ancestry was 33.3% in Forros, 27.3% in Tongas and approximately two-fold less, 14.5%, in Angolares. The Angolares also showed the lowest haplogroup diversity and the most reduced number of different haplogroups. The current results reinforce our previous evidence pointing to remarkable restrictions in gene flow between Angolares and other São Tomean inhabitants, in agreement with their considerable isolation and confinement to the south-eastern tip of São Tomé until recently.
Annals of Human Genetics 02/2007; 71(Pt 1):77-85. · 2.57 Impact Factor
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ABSTRACT: Follicular thyroid tumors are often aneuploid. It was advanced that chromosomal instability is closely associated to RAS mutations, but such association remains unproven. H-RAS can be alternatively spliced in two different proteins, p21 and p19, the former being the active protein. In order to investigate the relationship between RAS mutational status and ploidy in thyroid tumors, we analysed RAS genes in a series of 99 follicular lesions (14 nodular goiters, 70 follicular adenomas and 15 follicular carcinomas), eight thyroid carcinoma cell lines and a control group of 102 blood donors, correlating the presence of RAS mutations with the ploidy of the tumors and evaluating the two spliced forms of H-RAS. Overall, 20% of the follicular tumors harbored RAS mutations and 62% of the patients with follicular tumors (and 51% of blood donors) harbored the H-RAS 81T --> C polymorphism. The presence of RAS mutations was not associated with aneuploidy. The H-RAS polymorphism did not seem to confer a higher propensity for neoplastic transformation as it was also found in hyperplastic lesions, but was strongly associated with aneuploidy (P<0.0001). The presence of the H-RAS 81T --> C polymorphism was associated with significantly higher amounts of total H-RAS mRNA expression, higher amounts of p21 isoform and a higher fraction of neoplastic cells in S phase. Our results suggest that the H-RAS 81T --> C polymorphism may induce aneuploidy through overexpression of the active p21 isoform of H-RAS.
Oncogene 09/2006; 25(33):4620-7. · 6.37 Impact Factor
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L Gusmão,
J M Butler,
A Carracedo,
P Gill,
M Kayser,
W R Mayr,
N Morling,
M Prinz,
L Roewer,
C Tyler-Smith,
P M Schneider
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ABSTRACT: The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods
Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 08/2006; 120(4):191-200. · 2.59 Impact Factor
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Forensic Science International 02/2006; 156(2-3):261-5. · 2.30 Impact Factor
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ABSTRACT: Allele frequencies for the fifteen STRs included in the AmpF/STR Identifiler (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPO and VWA) were estimated from a sample of 186 unrelated individuals from East Timor. No deviations from Hardy-Weinberg equilibrium were observed (only after applying the Bonferroni correction in the cases of D2S1338, TPO and D5S818). Genetic parameters of forensic interest were calculated and comparison with geographically nearby populations was performed.
Forensic Science International 01/2006; 155(1):77-80. · 2.30 Impact Factor
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L Gusmão,
P Sánchez-Diz,
F Calafell,
P Martín,
C A Alonso,
F Alvarez-Fernández,
C Alves,
L Borjas-Fajardo,
W R Bozzo,
M L Bravo, [......],
G Vallejo,
L Vidal Rioja,
M C Vide,
C I Vieira da Silva,
M R Whittle,
W Zabala,
M T Zarrabeitia,
A Alonso,
A Carracedo,
A Amorim
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ABSTRACT: A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) to estimate Y-STR mutation rates. Seventeen Y chromosome STR loci (DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635 [GATA C4], GATA H4, and GATA A10) were analyzed in a sample of 3,026 father/son pairs. Among 27,029 allele transfers, 54 mutations were observed, with an overall mutation rate across the 17 loci of 1.998 x 10(-3) (95% CI, 1.501 x 10(-3) to 2.606 x 10(-3)). With just one exception, all of the mutations were single-step, and they were observed only once per gametogenesis. Repeat gains were more frequent than losses, longer alleles were found to be more mutable, and the mutation rate seemed to increase with the father's age. Hum Mutat 26(6), 520-528, 2005. (c) 2005 Wiley-Liss, Inc.
Human Mutation 01/2006; 26(6):520-8. · 5.69 Impact Factor
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ABSTRACT: In a genetic study of unrelated donors from Bahia (Brazil), one sample contained a 16 Y-STR haplotype with double peaks at three loci: DYS389 II, DYS437 and DYS439. The son of the subject had the same haplotype as found in the father. This profile was compared with a similar case found in a paternity case investigation in Madrid (Spain) and a match was found for the full 16 Y-STR haplotype. Because these three loci are located within the AZFa segment, these results are in accordance with duplication of the AZFa region that includes also other Y-STRs currently used in forensic investigation, for example DYS389I and DYS438. This case attracts our attention in the forensic interpretation of Y-haplotype profiles, because multiple alleles at various loci do not indicate forcibly that the sample under analysis is a mixture.
Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 08/2005; 119(4):223-5. · 2.59 Impact Factor
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A Alonso,
C Alves,
M P Suárez-Mier,
C Albarrán,
L Pereira,
L Fernández de Simón,
P Martín,
O García, L Gusmão,
M Sancho,
A Amorim
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ABSTRACT: DNA typing was requested to investigate a presumptive cancer diagnosis error by confirming whether benign and cancerous prostatic tissue in the same presurgical haematoxylin and eosin stained slide belonged to the same person. After independent histological re-examination of the slide by a pathologist, manual slide dissection was used to guarantee independent and high recovery DNA isolation from each tissue section, avoiding carryover and background contamination. Nuclear DNA quantification performed by real time polymerase chain reaction (PCR) revealed the absence of human DNA for short tandem repeat (STR) typing. Mitochondrial DNA was only obtained by performing PCR of very short fragments ( approximately 100 bp), indicating high DNA degradation. Different low frequency hypervariable region I haplotypes were obtained from each tissue section (normal tissue section haplotype: 16224C, 16234T, 16311C, 16356C; cancer tissue section haplotype: 16256T, 16270T, 16293G). Only the normal tissue section haplotype matched that obtained from the patient's blood sample, indicating that the cancer tissue section originated from an unknown patient. These results supported the hypothesis of sample mix up during block processing or slide preparation by a carryover mechanism. Mitochondrial genetic typing is recommended to exclude the possibility of carryover artefacts when low DNA content and high degradation compromise conventional STR typing.
Journal of Clinical Pathology 02/2005; 58(1):83-6. · 2.31 Impact Factor
