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Antão-Sousa S, Gusmão L, Modesti NM, Feliziani S, Faustino M, Marcucci V, Sarapura C, Ribeiro J, Carvalho E, Pereira V, Tomas C, de Pancorbo MM, Baeta M, Alghafri R, Almheiri R, Builes JJ, Gouveia N, Burgos G, Pontes MDL, Ibarra A, da Silva CV, Parveen R, Benitez M, Amorim A, Pinto N. Microsatellites' mutation modeling through the analysis of the Y-chromosomal transmission: Results of a GHEP-ISFG collaborative study. Forensic Sci Int Genet 2024; 69:102999. [PMID: 38181588 DOI: 10.1016/j.fsigen.2023.102999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/25/2023] [Accepted: 12/10/2023] [Indexed: 01/07/2024]
Abstract
The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) organized a collaborative study on mutations of Y-chromosomal short tandem repeats (Y-STRs). New data from 2225 father-son duos and data from 44 previously published reports, corresponding to 25,729 duos, were collected and analyzed. Marker-specific mutation rates were estimated for 33 Y-STRs. Although highly dependent on the analyzed marker, mutations compatible with the gain or loss of a single repeat were 23.2 times more likely than those involving a greater number of repeats. Longer alleles (relatively to the modal one) showed to be nearly twice more mutable than the shorter ones. Within the subset of longer alleles, the loss of repeats showed to be nearly twice more likely than the gain. Conversely, shorter alleles showed a symmetrical trend, with repeat gains being twofold more frequent than reductions. A positive correlation between the paternal age and the mutation rate was observed, strengthening previous findings. The results of a machine learning approach, via logistic regression analyses, allowed the establishment of algebraic formulas for estimating the probability of mutation depending on paternal age and allele length for DYS389I, DYS393 and DYS627. Algebraic formulas could also be established considering only the allele length as predictor for DYS19, DYS389I, DYS389II-I, DYS390, DYS391, DYS393, DYS437, DYS439, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS576, DYS626 and DYS627 loci. For the remaining Y-STRs, a lack of statistical significance was observed, probably as a consequence of the small effective size of the subsets available, a common difficulty in the modeling of rare events as is the case of mutations. The amount of data used in the different analyses varied widely, depending on how the data were reported in the publications analyzed. This shows a regrettable waste of produced data, due to inadequate communication of the results, supporting an urgent need of publication guidelines for mutation studies.
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Affiliation(s)
- Sofia Antão-Sousa
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal; DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Nidia M Modesti
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Sofía Feliziani
- Centro de Genética Forense, Poder Judicial de Córdoba, Argentina
| | - Marisa Faustino
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Valeria Marcucci
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Claudia Sarapura
- Laboratorio Regional de Investigación Forense, Tribunal Superior de Justicia de Santa Cruz, Argentina
| | - Julyana Ribeiro
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Elizeu Carvalho
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Lascaray Research Center, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Rashed Alghafri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Reem Almheiri
- International Center for Forensic Sciences, Dubai Police G.H.Q., Dubai, United Arab Emirates
| | - Juan José Builes
- GENES SAS Laboratory, Medellín, Colombia; Institute of Biology, University of Antioquia, Medellín, Colombia
| | - Nair Gouveia
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Centro, Portugal
| | - German Burgos
- One Health Global Research Group, Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador; Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria de Lurdes Pontes
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Norte, Portugal
| | - Adriana Ibarra
- Laboratorio IDENTIGEN, Universidad de Antioquia, Colombia
| | - Claudia Vieira da Silva
- Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. / Serviço de Genética e Biologia Forenses, Delegação do Sul, Portugal
| | - Rukhsana Parveen
- Forensic Services Laboratory, Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Marc Benitez
- Policia de la Generalitat de Catalunya - Mossos d'Esquadra. Unitat Central del Laboratori Biològic, Barcelona, Spain
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Centre of Mathematics of the University of Porto, Porto, Portugal.
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Tomas C, Rodrigues P, Jønck CG, Barekzay Z, Simayijiang H, Pereira V, Børsting C. Performance of a 74-Microhaplotype Assay in Kinship Analyses. Genes (Basel) 2024; 15:224. [PMID: 38397213 PMCID: PMC10888013 DOI: 10.3390/genes15020224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.
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Affiliation(s)
| | | | | | | | | | | | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V’s Vej 11, DK-2100 Copenhagen, Denmark; (C.T.); (P.R.); (C.G.J.); (Z.B.); (V.P.)
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Garcia-Garcia C, Andrea R, Sanz E, Sanchez-Salado JC, Aboal J, Pastor P, Buera I, Sionis A, Lopez T, Perez-Rodriguez M, Ariza A, Baneras J, Tomas C, Cediel G, Rueda F. Mortality risk in cardiogenic shock depending on aetiology in a Mediterranean cohort. Prognostic accuracy of CardShock vs IABP score: the Shock CAT study. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Mortality in cardiogenic shock (CS) remains very high. Several risk scores have been purposed to early stratification, although the CS aetiology could influence in this prediction.
Purpose
The aim is to investigate in-hospital prognosis and mortality risk in CS patients depending on the CS aetiology comparing the prognostic accuracy of CardShock and IABP scores in a Mediterranean cohort.
Method
Shock CAT study was a multicentre, prospective, observational study conducted between December 2018 and December 2019 in eight public University hospitals in Catalonia (Spain), including CS patients due to acute coronary syndrome (ACS) and other aetiologies. Data on clinical presentation, biomarkers, management, including mechanical assistance support were analyzed comparing ACS and non-ACS patients. Cardshock and IABP score have been compared to assess 90-days mortality risk in both groups.
Results
A total of 382 CS patients were included, mean age was 65.3 (SD 13.9) years and 75.1% were men. Patient were classified in ACS (n=232, 60.7%) and non-ACS (n=150, 39.3%). In ACS group, 77.6% were STEMI, reperfussion in 84.7% of cases, all with primary angioplasty, 9% developed mechanical complications and 19.4% primary ventricular fibrillation. Main non-ACS aetiologies were severe heart failure (36.2%), malignant arrhythmias (22.1%), valve disease (8.0%) and myocarditis (7.4%). ACS group had less prevalence of women (17.7% vs 36%, p=0.001) and previous myocardial infarction (13.9% vs 24.8%, p=0.007). Mechanical assistance device was implanted more in ACS patients (43.1% vs 16.7%, p<0.001, mainly intraaortic balloon pump (35.6% vs 9.8%, p<0.001) and ECMO (10.7% vs 3%, p=0.01). Both shock risk scores were higher in ACS patients, Cardshock (4.5 vs 4.0, p=0.006) and IABP (2.4 vs 1.9, p=0.005). In-hospital mortality was higher in ACS (37.1 vs 26.7%, p=0.035) although this difference loss the significance at 90-days (40.9 vs 31.8%, p=0.074) and 6-months (45.2 vs 35.8%, p=0.176). Receiver-operating characteristic curves demonstrated that IABP shock score had superior prognostic power for predicting 90-days mortality when compared with Cardshock score in ACS patients (area under the curve -AUC- 0.74 vs 0.66) respectively, p=0.047, although both scores were similar in non-ACS (AUC 0.64 vs 0.62, p=0.693), Figures 1–2.
Conclusions
Cardiogenic shock due to ACS had higher in-hospital mortality than non-ACS CS, although this difference decreased at 90 days and 6 months. IABP score provided better 90-days mortality risk prediction than CardShock score in ACS patients, but both scores are similar in non-ACS cardiogenic shock.
Funding Acknowledgement
Type of funding sources: None. Figure 1Figure 2
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Affiliation(s)
| | - R Andrea
- Hospital Clinic de Barcelona, Barcelona, Spain
| | - E Sanz
- University Hospital of Taragona Joan XXIII, Tarragona, Spain
| | | | - J Aboal
- University Hospital de Girona Dr. Josep Trueta, Regiό Sanitaria de Girona, Girona, Spain
| | - P Pastor
- Hospital Arnau de Vilanova, Lleida, Spain
| | - I Buera
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - A Sionis
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - T Lopez
- Hospital Clinic de Barcelona, Barcelona, Spain
| | | | - A Ariza
- Hospital Universitari de Bellvitge, Barcelona, Spain
| | - J Baneras
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - C Tomas
- Hospital Arnau de Vilanova, Lleida, Spain
| | - G Cediel
- Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - F Rueda
- Germans Trias i Pujol University Hospital, Barcelona, Spain
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Garcia-Garcia C, Lopez T, Sanz E, Sanchez-Salado JC, Aboal J, Tomas C, Baneras J, Sionis A, Andrea R, Perez-Rodriguez M, Ariza A, Pastor P, Buera I, Cediel G, Rueda F. Mortality risk in cardiogenic shock: head to head comparision CardShock vs IABP score in a Mediterranean cohort: the Shock CAT study. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Mortality in cardiogenic shock (CS) remains very high. Several risk scores have been purposed to early stratification.
Purpose
The aim is to investigate in-hospital prognosis and mortality risk in CS patients comparing the prognostic accuracy of CardShock and IABP scores in a Mediterranean cohort.
Method
Shock CAT study was a multicentre, prospective, observational study conducted between December 2018 and December 2019 in eight public University hospitals in Catalonia (Spain), including CS patients due to acute coronary syndrome (ACS) and other aetiologies. Data on clinical presentation, biomarkers, management, including mechanical assistance support were analyzed. Cardshock and IABP score have been compared to assess 90-days mortality risk in a Mediterranean cohort.
Results
A total of 382 CS patients were included, mean age was 65.3 (SD 13.9) years and 75.1% were men. The most common cause of CS was ACS (61%, n=233); of them, 77.6% were STEMI, 9% developed mechanical complications and 19.4% primary ventricular fibrillation. STEMI patients were reperfused in 84.7% of cases, all with primary angioplasty. Main non-ACS aetiologies were severe acute heart failure, malignant arrhythmias and myocarditis. Mechanical assistance device was implanted in one third of patients (n=119), mainly intraaortic balloon pump (26.1%), ECMO in 7.8% and Impella in 4.5%. Average Cardshock score was 4.3 (SD 1.74) and mean IABP score was 2.2 (SD 1.61). In-hospital mortality was 33% (126 patients) and 90-days mortality was 37.3% (141 patients). Receiver-operating characteristic curves demonstrated that IABP shock score had superior prognostic power for predicting 90-days mortality when compared with Cardshock score (area under the curve 0.72 vs 0.66) respectively, p=0.042; Figure 1.
Conclusions
Even though invasive management with STEMI reperfusion and mechanical assistance devices, cardiogenic shock in-hospital mortality remains 33% in a contemporary Mediterranean cohort. In this population, IABP shock score provided better 90-days mortality risk prediction than CardShock score
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
| | - T Lopez
- Hospital Clinic de Barcelona, Barcelona, Spain
| | - E Sanz
- University Hospital of Taragona Joan XXIII, Tarragona, Spain
| | | | - J Aboal
- University Hospital de Girona Dr. Josep Trueta, Girona, Spain
| | - C Tomas
- Hospital Arnau de Vilanova, Lleida, Spain
| | - J Baneras
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - A Sionis
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - R Andrea
- Hospital Clinic de Barcelona, Barcelona, Spain
| | | | - A Ariza
- Hospital Universitari de Bellvitge, Barcelona, Spain
| | - P Pastor
- Hospital Arnau de Vilanova, Lleida, Spain
| | - I Buera
- University Hospital Vall d'Hebron, Barcelona, Spain
| | - G Cediel
- Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - F Rueda
- Germans Trias i Pujol University Hospital, Barcelona, Spain
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Tomas C, Poulsen L, Drobnič K, Ivanova V, Jankauskiene J, Bunokiene D, Børsting C, Morling N. Thirty autosomal insertion-deletion polymorphisms analyzed using the Investigator ® DIPplex Kit in populations from Iraq, Lithuania, Slovenia, and Turkey. Forensic Sci Int Genet 2016; 25:142-144. [PMID: 27599378 DOI: 10.1016/j.fsigen.2016.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/29/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Thirty autosomal insertion-deletion (InDel) polymorphisms were analyzed in four populations from Iraq, Lithuania, Slovenia, and Turkey using the commercial kit Investigator® DIPplex. Genotyping issues were encountered for five of the 30 InDels. They were most probably caused by polymorphisms located in the primer binding sites. Population and forensic parameters were calculated. No significant deviations from Hardy-Weinberg equilibrium or significant linkage disequilibrium were detected. The observed heterozygosities ranged from 33% to 61% depending on the marker and the population. The combined probability of exclusion for the 30 markers was 99.7% in all four populations and the matching probabilities were 1 in 3-4×1012 individuals. The multidimensional scaling plot drawn from FST distances showed a good concordance between the relative position of the 15 populations included in the plot and their geographic locations.
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Affiliation(s)
- C Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark.
| | - L Poulsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark
| | - K Drobnič
- National Forensic Laboratory, Police, Ministry of the Interior, Vodovodna 95, 1000 Ljubljana, Slovenia
| | - V Ivanova
- State Forensic Medicine Service under the Ministry of Justice of the Republic of Lithuania, Vilnius, Lithuania
| | - J Jankauskiene
- State Forensic Medicine Service under the Ministry of Justice of the Republic of Lithuania, Vilnius, Lithuania
| | - D Bunokiene
- State Forensic Medicine Service under the Ministry of Justice of the Republic of Lithuania, Vilnius, Lithuania
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100, Copenhagen, Denmark
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Poulsen L, Tomas C, Drobnič K, Ivanova V, Mogensen H, Kondili A, Miniati P, Bunokiene D, Jankauskiene J, Pereira V, Morling N. NGMSElect™ and Investigator ® Argus X-12 analysis in population samples from Albania, Iraq, Lithuania, Slovenia, and Turkey. Forensic Sci Int Genet 2016; 22:110-112. [DOI: 10.1016/j.fsigen.2016.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/29/2016] [Accepted: 02/09/2016] [Indexed: 11/25/2022]
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Benaissa A, Tomas C, Clarençon F, Sourour N, Herbreteau D, Spelle L, Gallas S, Januel AC, Gaultier AL, Pierot L. Retrospective Analysis of Delayed Intraparenchymal Hemorrhage after Flow-Diverter Treatment: Presentation of a Retrospective Multicenter Trial. AJNR Am J Neuroradiol 2015; 37:475-80. [PMID: 26514605 DOI: 10.3174/ajnr.a4561] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/29/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Intracranial aneurysm treatment with flow diverters has shown satisfying results in terms of aneurysm occlusion, and while some cases of delayed intraparenchymal hemorrhage have been described, no systematic analysis of the risk factors affecting its occurrence has been conducted in a large series of patients. This retrospective analysis of delayed intraparenchymal hemorrhage after flow-diverter treatment is a multicenter, retrospective study using a large series of treated patients to analyze factors affecting the occurrence of delayed intraparenchymal hemorrhage. MATERIALS AND METHODS Patients treated with flow diverters and presenting with delayed intraparenchymal hemorrhage were included from December 2007 to December 2014 in 7 participating centers in France. Patient and aneurysm characteristics were recorded as were characteristics of bleeding (size, lateralization, and time to bleed), treatment, and clinical outcome after 1, 3, and 6 months. RESULTS Delayed intraparenchymal hemorrhage occurred in 11 patients between 1 and 21 days after the procedure. In 10 of these patients, hemorrhages were ipsilateral to the treated aneurysms. Five of the 11 underwent surgery, and 9 of the 11 had good clinical outcomes at 6 months (mRS ≤2). CONCLUSIONS The pathogenesis of delayed intraparenchymal hemorrhage occurring after flow-diverter treatment remains unclear. The multidisciplinary management of delayed intraparenchymal hemorrhage yields a relatively low morbidity-mortality rate compared with the initial clinical presentation.
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Affiliation(s)
- A Benaissa
- From the Department of Neuroradiology (A.B., C.T., L.P.), Centres Hospitaliers Universitaires de Reims, Reims, France
| | - C Tomas
- From the Department of Neuroradiology (A.B., C.T., L.P.), Centres Hospitaliers Universitaires de Reims, Reims, France
| | - F Clarençon
- Department of Neuroradiology (F.C., N.S.), Centres Hospitaliers Universitaires of Pitié-Salpêtrière, Paris, France
| | - N Sourour
- Department of Neuroradiology (F.C., N.S.), Centres Hospitaliers Universitaires of Pitié-Salpêtrière, Paris, France
| | - D Herbreteau
- Department of Neuroradiology (D.H.), Centres Hospitaliers Universitaires of Tours, Tours, France
| | - L Spelle
- Department of Neuroradiology (L.S.), Centres Hospitaliers Universitaires of Beaujon, Clichy, France
| | - S Gallas
- Department of Neuroradiology (S.G.), Centres Hospitaliers Universitaires of Créteil, Créteil, France
| | - A-C Januel
- Department of Neuroradiology (A.-C.J.), Centres Hospitaliers Universitaires of Toulouse, Toulouse, France
| | - A L Gaultier
- Department of Neuroradiology (A.L.G.), Centres Hospitaliers Universitaires of Nantes, Nantes, France
| | - L Pierot
- From the Department of Neuroradiology (A.B., C.T., L.P.), Centres Hospitaliers Universitaires de Reims, Reims, France
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Tomas C, Skitsa I, Steinmeier E, Poulsen L, Ampati A, Børsting C, Morling N. Results for five sets of forensic genetic markers studied in a Greek population sample. Forensic Sci Int Genet 2015; 16:132-137. [DOI: 10.1016/j.fsigen.2015.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 12/16/2014] [Accepted: 01/02/2015] [Indexed: 11/30/2022]
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Pereira V, Tomas C, Sanchez JJ, Syndercombe-Court D, Amorim A, Gusmão L, Prata MJ, Morling N. The peopling of Greenland: further insights from the analysis of genetic diversity using autosomal and X-chromosomal markers. Eur J Hum Genet 2014; 23:245-51. [PMID: 24801759 DOI: 10.1038/ejhg.2014.90] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 11/09/2022] Open
Abstract
The peopling of Greenland has a complex history shaped by population migrations, isolation and genetic drift. The Greenlanders present a genetic heritage with components of European and Inuit groups; previous studies using uniparentally inherited markers in Greenlanders have reported evidence of a sex-biased, admixed genetic background. This work further explores the genetics of the Greenlanders by analysing autosomal and X-chromosomal data to obtain deeper insights into the factors that shaped the genetic diversity in Greenlanders. Fourteen Greenlandic subsamples from multiple geographical settlements were compared to assess the level of genetic substructure in the Greenlandic population. The results showed low levels of genetic diversity in all sets of the genetic markers studied, together with an increased number of X-chromosomal loci in linkage disequilibrium in relation to the Danish population. In the broader context of worldwide populations, Greenlanders are remarkably different from most populations, but they are genetically closer to some Inuit groups from Alaska. Admixture analyses identified an Inuit component in the Greenlandic population of approximately 80%. The sub-populations of Ammassalik and Nanortalik are the least diverse, presenting the lowest levels of European admixture. Isolation-by-distance analyses showed that only 16% of the genetic substructure of Greenlanders is most likely to be explained by geographic barriers. We suggest that genetic drift and a differentiated settlement history around the island explain most of the genetic substructure of the population in Greenland.
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Affiliation(s)
- Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø, Denmark
| | - Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø, Denmark
| | - Juan J Sanchez
- Instituto Nacional de Toxicología y Ciencias Forenses, Delegación de Canarias, La Cuesta, Tenerife, Spain
| | - Denise Syndercombe-Court
- Academic Haematology, Blizard Institute, Barts and the London School of Medicine and Dentistry, London, UK
| | - António Amorim
- 1] IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal [2] Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Leonor Gusmão
- 1] IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal [2] DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - Maria João Prata
- 1] IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal [2] Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen Ø, Denmark
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Tomas C, Mogensen HS, Friis SL, Hallenberg C, Stene MC, Morling N. Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex® ESI 17 and AmpFℓSTR® NGM SElect™ in Somalis, Danes and Greenlanders. Forensic Sci Int Genet 2014; 11:e18-21. [PMID: 24810256 DOI: 10.1016/j.fsigen.2014.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 12/01/2022]
Abstract
A concordance study of the results of PowerPlex(®) ESI 17 and AmpFℓSTR(®) NGM SElect™ kits obtained from 591 individuals from Somalia (N=198), Denmark (N=199) and Greenland (N=194) was performed. Among 9456 STR types, seven discordant results were found with the two kits: one observed in the D19S433 system in an individual from Denmark and six in the SE33 system in six individuals from Somalia. Sequencing of SE33 in the six samples with discordant results showed G>A transition 15bp downstream of the repeat unit in three of the individuals, and G>A transition 68bp downstream of the repeat unit in the other three individuals. Population data for 16 autosomal STR systems analyzed in 989 individuals from Somalia, Denmark and Greenland are also presented. The highest mean heterozygosity was observed in Danes (82.5%). With the exception of D8S1179 in Danes, no significant deviations from Hardy-Weinberg expectations were observed. Only one pair of systems (D12S391 and D18S51) showed significant allelic association in Greenlanders (after Holm-Šidák correction). A MDS plot drawn from pairwise FST values calculated between 21 populations showed a clear displacement of the Greenlandic population versus the other ones included in the analyses. The highest combined chance of exclusion and power of discrimination was observed for Danes reaching values of 99.9999987% and 1 in 1.8×10(21), respectively.
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Affiliation(s)
- C Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark.
| | - H S Mogensen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - S L Friis
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - C Hallenberg
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - M C Stene
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, DK-2100 Copenhagen, Denmark
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11
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Pereira V, Tomas C, Pietroni C, Andersen J, Fordyce S, Pinto N, Mikkelsen M, Børsting C, Amorim A, Gusmão L, Prata M, Morling N. Assessing the potential application of X-chromosomal haploblocks in population genetics and forensic studies. Forensic Science International: Genetics Supplement Series 2013. [DOI: 10.1016/j.fsigss.2013.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Tomas C, Diez IE, Moncada E, Børsting C, Morling N. Analysis of 49 autosomal SNPs in an Iraqi population. Forensic Sci Int Genet 2013; 7:198-9. [DOI: 10.1016/j.fsigen.2012.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/29/2012] [Accepted: 05/05/2012] [Indexed: 11/16/2022]
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13
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Børsting C, Tomas C, Morling N. Typing of 49 autosomal SNPs by single base extension and capillary electrophoresis for forensic genetic testing. Methods Mol Biol 2012; 830:87-107. [PMID: 22139655 DOI: 10.1007/978-1-61779-461-2_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
We describe a method for simultaneous amplification of 49 autosomal single nucleotide polymorphisms (SNPs) by multiplex PCR and detection of the SNP alleles by single base extension (SBE) and capillary electrophoresis. All the SNPs may be amplified from only 100 pg of genomic DNA and the length of the amplicons range from 65 to 115 bp. The high sensitivity and the short amplicon sizes make the assay very suitable for typing of degraded DNA samples, and the low mutation rate of SNPs makes the assay very useful for relationship testing. Combined, these advantages make the assay well suited for disaster victim identifications, where the DNA from the victims may be highly degraded and the victims are identified via investigation of their relatives. The assay was validated according to the ISO 17025 standard and used for routine case work in our laboratory.
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Affiliation(s)
- Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark.
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Friis SL, Børsting C, Rockenbauer E, Poulsen L, Fredslund SF, Tomas C, Morling N. Typing of 30 insertion/deletions in Danes using the first commercial indel kit—Mentype® DIPplex. Forensic Sci Int Genet 2012; 6:e72-4. [DOI: 10.1016/j.fsigen.2011.08.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 07/25/2011] [Accepted: 08/05/2011] [Indexed: 11/16/2022]
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Mignini Renzini M, Dal Canto M, Coticchio G, Novara P, Turchi D, Lain M, Guarnieri T, Brambillasca F, Fadini R, Lash GE, Innes BA, Drury JA, Quenby S, Bulmer JN, Goddijn M, Boogaard van den E, Scheenjes E, Kremer JAM, Veen van der F, Hermens RPMG, Vansenne F, De Borgie CAJM, Snijder S, Redeker EJW, Van Maarle MC, Wouters CH, Bruggenwirth HT, Van der Veen F, Bossuyt PMM, Goddijn M, Ledger W, Alsbjerg B, Tomas C, Martikainen H, Humaidan P. SESSION 05: EARLY PREGNANCY. Hum Reprod 2012. [DOI: 10.1093/humrep/27.s2.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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16
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Pereira V, Moncada E, Diez IE, Tomas C, Amorim A, Morling N, Gusmão L, Prata MJ. Genetic characterization of Somali and Iraqi populations using a set of 33 X-chromosome Indels. Forensic Science International: Genetics Supplement Series 2011. [DOI: 10.1016/j.fsigss.2011.08.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Pereira R, Pereira V, Gomes I, Tomas C, Morling N, Amorim A, Prata MJ, Carracedo A, Gusmão L. A method for the analysis of 32 X chromosome insertion deletion polymorphisms in a single PCR. Int J Legal Med 2011; 126:97-105. [PMID: 21717151 DOI: 10.1007/s00414-011-0593-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 06/16/2011] [Indexed: 12/11/2022]
Abstract
Studies of human genetic variation predominantly use short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) but Insertion deletion polymorphisms (Indels) are being increasingly explored. They combine desirable characteristics of other genetic markers, especially the possibility of being analysed using short amplicon strategies, which increases the ease of analysis, contributing to justify their interest in population and forensic genetics. After the advent of autosomal and uniparental genomes (mtDNA and Y chromosome), these fields of research are also focusing on the X chromosome, given its special transmission pattern. The X chromosome markers brought new insights into the history of modern human populations and also proved useful in forensic kinship investigations, namely in deficient relationship cases and in cases where autosomes are uninformative. This work describes an X-Indel multiplex system amplifying 32 biallelic markers in one single PCR. The multiplex includes X-Indels shown to be polymorphic in the major human population groups and follows a short amplicon strategy. The set was applied in the genetic characterization of sub-Saharan African, European and East Asian population samples and revealed high forensic efficiency, as measured by the accumulated power of discrimination (0.9999990 was the lowest value in males and 0.999999999998 was the highest in females) and mean exclusion chance varied between 0.998 and 0.9996 in duos and between 0.99997 and 0.999998 in trios. Finally, a segregation analysis was performed using trio constellations of father-mother-daughters in order to address the transmission pattern and assess mutation rates of this type of markers.
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Affiliation(s)
- Rui Pereira
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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Børsting C, Tomas C, Morling N. SNP typing of the reference materials SRM 2391b 1–10, K562, XY1, XX74, and 007 with the SNPforID multiplex. Forensic Sci Int Genet 2011; 5:e81-2. [DOI: 10.1016/j.fsigen.2010.07.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 11/25/2022]
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Castel M, Roig E, Tomas C, Farrero M, Martinez-Mateo V, Cardona M, Pérez-Villa F. 335 Elevated Heart Rate at Twelve Months after Heart Transplantation Is an Independent Predictor of Long Term Mortality. J Heart Lung Transplant 2011. [DOI: 10.1016/j.healun.2011.01.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Drobnič K, Børsting C, Rockenbauer E, Tomas C, Morling N. Typing of 49 autosomal SNPs by SNaPshot® in the Slovenian population. Forensic Sci Int Genet 2010; 4:e125-7. [DOI: 10.1016/j.fsigen.2010.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 01/19/2010] [Accepted: 01/21/2010] [Indexed: 11/27/2022]
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Tomas C, Axler-DiPerte G, Budimlija ZM, Børsting C, Coble MD, Decker AE, Eisenberg A, Fang R, Fondevila M, Fredslund SF, Gonzalez S, Hansen AJ, Hoff-Olsen P, Haas C, Kohler P, Kriegel AK, Lindblom B, Manohar F, Maroñas O, Mogensen HS, Neureuther K, Nilsson H, Scheible MK, Schneider PM, Sonntag ML, Stangegaard M, Syndercombe-Court D, Thacker CR, Vallone PM, Westen AA, Morling N. Autosomal SNP typing of forensic samples with the GenPlex™ HID System: results of a collaborative study. Forensic Sci Int Genet 2010; 5:369-75. [PMID: 20650697 DOI: 10.1016/j.fsigen.2010.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 06/24/2010] [Accepted: 06/24/2010] [Indexed: 10/19/2022]
Abstract
The GenPlex™ HID System (Applied Biosystems - AB) offers typing of 48 of the 52 SNPforID SNPs and amelogenin. Previous studies have shown a high reproducibility of the GenPlex™ HID System using 250-500pg DNA of good quality. An international exercise was performed by 14 laboratories (9 in Europe and 5 in the US) in order to test the robustness and reliability of the GenPlex™ HID System on forensic samples. Three samples with partly degraded DNA and 10 samples with low amounts of DNA were analyzed in duplicates using various amounts of DNA. In order to compare the performance of the GenPlex™ HID System with the most commonly used STR kits, 500pg of partly degraded DNA from three samples was typed by the laboratories using one or more STR kits. The median SNP typing success rate was 92.3% with 500pg of partly degraded DNA. Three of the fourteen laboratories counted for more than two thirds of the locus dropouts. The median percentage of discrepant results was 0.2% with 500pg degraded DNA. An increasing percentage of locus dropouts and discrepant results were observed when lower amounts of DNA were used. Different success rates were observed for the various SNPs. The rs763869 SNP was the least successful. With the exception of the MiniFiler™ kit (AB), GenPlex™ HID performed better than five other tested STR kits. When partly degraded DNA was analyzed, GenPlex™ HID showed a very low mean mach probability, while all STR kits except MiniFiler™ had very limited discriminatory power.
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Affiliation(s)
- C Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark.
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Tomas C, Sanchez JJ, Castro JA, Børsting C, Morling N. Forensic usefulness of a 25 X-chromosome single-nucleotide polymorphism marker set. Transfusion 2010; 50:2258-65. [DOI: 10.1111/j.1537-2995.2010.02696.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Tomas C, Bastisch I, Børsting C, Carracedo A, Coble M, Eisenberg A, Fang R, Frisk Fredslund S, Haas C, Hansen A, Hoff-Olsen P, Lindblom B, Mogensen H, Prinz M, Stangegaard M, Vallone P, Westen A, Morling N. SNP typing of forensic samples with the GenPlex™ HID system: A collaborative study. Forensic Science International: Genetics Supplement Series 2009. [DOI: 10.1016/j.fsigss.2009.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Hallenberg C, Tomas C, Simonsen B, Morling N. Y-chromosome STR haplotypes in males from Greenland. Forensic Sci Int Genet 2009; 3:e145-6. [PMID: 19647703 DOI: 10.1016/j.fsigen.2008.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 11/26/2008] [Accepted: 11/29/2008] [Indexed: 11/27/2022]
Abstract
A total of 272 males from Greenland were typed for 11 Y-chromosome STRs DYS19, DYS385a/b, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 with the PowerPlex Y System (Promega). A total of 146 different haplotypes were observed and the haplotype diversity was 0.9887. The number of haplotypes seen once was 108 and the most common haplotype was observed in 12 males. A significant F(ST) value was observed (F(ST)=0.012, P<0.00001) when comparing the population of 15 locations in Greenland assigned to 7 groups. The significance could mainly be attributed to the subpopulation of males from Tasiilaq (East of Greenland). The R(ST) value was not statistically significant (R(ST)=0.016, P=0.15).
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Affiliation(s)
- Charlotte Hallenberg
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark
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25
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Devroey P, Aboulghar M, Garcia-Velasco J, Griesinger G, Humaidan P, Kolibianakis E, Ledger W, Tomas C, Fauser BC. Improving the patient's experience of IVF/ICSI: a proposal for an ovarian stimulation protocol with GnRH antagonist co-treatment. Hum Reprod 2008; 24:764-74. [DOI: 10.1093/humrep/den468] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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26
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Tomas C, Stangegaard M, Børsting C, Hansen AJ, Morling N. Typing of 48 autosomal SNPs and amelogenin with GenPlex SNP genotyping system in forensic genetics. Forensic Sci Int Genet 2008; 3:1-6. [PMID: 19083859 DOI: 10.1016/j.fsigen.2008.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Revised: 06/19/2008] [Accepted: 06/30/2008] [Indexed: 11/30/2022]
Abstract
GenPlex (Applied Biosystems) is a new SNP genotyping system based on an initial PCR amplification followed by an oligo ligation assay (OLA). The OLA consists of the hybridization of allele and locus specific oligonucleotides (ASOs and LSOs) to PCR products and posterior ligation of ASOs and LSOs. The ligation products are immobilized to microtitre plates and reporter oligonucleotides (ZipChute probes) are hybridized to the ligation products. ZipChute probes are subsequently eluted and detected using capillary electrophoresis. Applied Biosystems developed the GenPlex SNP genotyping system with amelogenin and 48 of the 52 SNPs used in the 52 SNP-plex assay developed by the SNPforID consortium. The system requires equipment that is usually found in forensic genetic laboratories. The use of a robot for performance of the pipetting steps is highly recommendable. A total of 286 individuals from Denmark, Somalia and Greenland were investigated with GenPlex using a Biomek 3000 (Beckman Coulter) robot. The results were compared to results obtained with an ISO 17025 accredited SNP typing assay based on single base extension (SBE). With the GenPlex SNP genotyping system, full SNP profiles were obtained in 97.6% of the investigations. Perfect concordance was obtained in duplicate investigations and the SNP genotypes obtained with the GenPlex system were concordant with those of the accredited SBE based SNP typing system except for one result in rs901398 in one of 286 individuals most likely due to a mutation 6 bp downstream of the SNP. Reproducible SNP genotypes were obtained from as little as 250 pg of DNA.
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Affiliation(s)
- Carmen Tomas
- Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, 11 Frederik V's Vej, DK-2100 Copenhagen, Denmark.
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Tomas C, Sanchez JJ, Barbaro A, Brandt-Casadevall C, Hernandez A, Ben Dhiab M, Ramon M, Morling N. X-chromosome SNP analyses in 11 human Mediterranean populations show a high overall genetic homogeneity except in North-west Africans (Moroccans). BMC Evol Biol 2008; 8:75. [PMID: 18312628 PMCID: PMC2315647 DOI: 10.1186/1471-2148-8-75] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 02/29/2008] [Indexed: 11/20/2022] Open
Abstract
Background Due to its history, with a high number of migration events, the Mediterranean basin represents a challenging area for population genetic studies. A large number of genetic studies have been carried out in the Mediterranean area using different markers but no consensus has been reached on the genetic landscape of the Mediterranean populations. In order to further investigate the genetics of the human Mediterranean populations, we typed 894 individuals from 11 Mediterranean populations with 25 single-nucleotide polymorphisms (SNPs) located on the X-chromosome. Results A high overall homogeneity was found among the Mediterranean populations except for the population from Morocco, which seemed to differ genetically from the rest of the populations in the Mediterranean area. A very low genetic distance was found between populations in the Middle East and most of the western part of the Mediterranean Sea. A higher migration rate in females versus males was observed by comparing data from X-chromosome, mt-DNA and Y-chromosome SNPs both in the Mediterranean and a wider geographic area. Multilocus association was observed among the 25 SNPs on the X-chromosome in the populations from Ibiza and Cosenza. Conclusion Our results support both the hypothesis of (1) a reduced impact of the Neolithic Wave and more recent migration movements in NW-Africa, and (2) the importance of the Strait of Gibraltar as a geographic barrier. In contrast, the high genetic homogeneity observed in the Mediterranean area could be interpreted as the result of the Neolithic wave caused by a large demic diffusion and/or more recent migration events. A differentiated contribution of males and females to the genetic landscape of the Mediterranean area was observed with a higher migration rate in females than in males. A certain level of background linkage disequilibrium in populations in Ibiza and Cosenza could be attributed to their demographic background.
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Affiliation(s)
- Carmen Tomas
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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West NJ, Bacchieri R, Hansen G, Tomas C, Lebaron P, Moreau H. Rapid quantification of the toxic alga Prymnesium parvum in natural samples by use of a specific monoclonal antibody and solid-phase cytometry. Appl Environ Microbiol 2006; 72:860-8. [PMID: 16391128 PMCID: PMC1352178 DOI: 10.1128/aem.72.1.860-868.2006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing incidence of harmful algal blooms around the world and their associated health and economic effects require the development of methods to rapidly and accurately detect and enumerate the target species. Here we describe use of a solid-phase cytometer to detect and enumerate the toxic alga Prymnesium parvum in natural samples, using a specific monoclonal antibody and indirect immunofluorescence. The immunoglobulin G antibody 16E4 exhibited narrow specificity in that it recognized several P. parvum strains and a Prymnesium nemamethecum strain but it did not cross-react with P. parvum strains from Scandinavia or any other algal strains, including species of the closely related genus Chrysochromulina. Prymnesium sp. cells labeled with 16E4 were readily detected by the solid-phase cytometer because of the large fluorescence signal and the signal/noise ratio. Immunofluorescence detection and enumeration of cultured P. parvum cells preserved with different fixatives showed that the highest cell counts were obtained when cells were fixed with either glutaraldehyde or formaldehyde plus the cell protectant Pluronic F-68, whereas the use of formaldehyde alone resulted in significantly lower counts. Immunofluorescence labeling and analysis with the solid-phase cytometer of fixed natural samples from a bloom of P. parvum occurring in Lake Colorado in Texas gave cell counts that were close to those obtained by the traditional method of counting using light microscopy. These results show that a solid-phase cytometer can be used to rapidly enumerate natural P. parvum cells and that it could be used to detect other toxic algae, with an appropriate antibody or DNA probe.
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Affiliation(s)
- N J West
- Laboratoire Arago, UMR CNRS-Université Paris VI 7628/7621, Banyuls sur mer, France
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Abstract
OBJECTIVE To determine the relationship between perception of aggression, personality disorders and psychiatric morbidity. METHOD Ninety nursing students were interviewed. A two-stage transversal analysis was used, the first stage using the Spanish version of the general health questionnaire (GHQ-28), the true-false test of international personality disorders (IPDE) of Loranger, and the perception of aggression scale (POAS) of Jansen. For the second stage we used the Spanish version of the clinical interview schedule (CIS), and the full test of IPDE. RESULTS Perception of aggression was mainly described as a violent reaction. There were no significant differences in the perception of aggression according to GHQ(+), CIS(+) and IPDE(+). There was a significant relationship between perception of aggression as violent reaction and gender. CONCLUSION Aggression was perceived by our nursing students as a violent reaction. A significant relationship with gender was observed.
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Affiliation(s)
- C Muro
- Department of Nursing, University School of Health Sciences, University of Zaragoza, Spain
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Erra A, Tomas C, Barcelo P, Vilardell M, Marsal S. Is the recommended dose of leflunomide the best regimen to treat rheumatoid arthritis patients? Rheumatology (Oxford) 2003; 42:1123-4. [PMID: 12923276 DOI: 10.1093/rheumatology/keg292] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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31
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Albeza MV, Picornell A, Acreche N, Tomas C, Castro JA, Ramon MM. Genetic variability at 14 STR loci in the Puna population of north western Argentina. Int J Legal Med 2002; 116:126-32. [PMID: 12111314 DOI: 10.1007/s00414-001-0268-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Frequency data of the short tandem repeat (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, HUMTH01, D4S243, D18S535, HUMF13A1 and D12S391 were determined in the Puna population (Andean region from north western Argentina). In this study, 5 out of the 14 loci did not meet Hardy-Weinberg expectations. The excess of homozygotes observed in most of the markers could be due to a Wahlund effect and/or inbreeding. The frequencies were significantly different from those of other compared populations from Europe and America. Forensic parameters indicated that the 14 loci studied in the Puna region are highly discriminating, but the lack of Hardy-Weinberg equilibrium in some of the markers must be taken into account in the application of these results to paternity and forensic casework.
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Affiliation(s)
- M V Albeza
- Facultad de Ciencias Naturales, Facultad de Humanidades y CIUNSa, Universidad Nacional de Salta, Argentina, Bs. As. 177 (4400) Salta, Argentina
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Nuojua-Huttunen S, Tomas C, Bloigu R, Tuomivaara L, Martikainen H. Intrauterine insemination treatment in subfertility: an analysis of factors affecting outcome. Hum Reprod 1999; 14:698-703. [PMID: 10221698 DOI: 10.1093/humrep/14.3.698] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A total of 811 intrauterine insemination (IUI) cycles in which clomiphene citrate/human menopausal gonadotrophin (HMG) was used for ovarian stimulation were analysed retrospectively to identify prognostic factors regarding treatment outcome. The overall pregnancy rate was 12.6% per cycle, the multiple pregnancy rate 13.7%, and the miscarriage rate 23.5%. Logistic regression analysis revealed five predictive variables as regards pregnancy: number of the treatment cycle (P = 0.009), duration of infertility (P = 0.017), age (P = 0.028), number of follicles (P = 0.031) and infertility aetiology (P = 0.045). The odds ratios for age < 40 years, unexplained infertility aetiology (versus endometriosis) and duration of infertility < or = 6 years were 3.24, 2.79 and 2.33, respectively. A multifollicular ovarian response to clomiphene citrate/HMG resulted in better treatment success than a monofollicular response, and 97% of the pregnancies were obtained in the first four treatment cycles. The results indicate that clomiphene citrate/HMG/IUI is a useful and cost-effective treatment option in women < 40 years of age with infertility duration < or = 6 years, who do not suffer from endometriosis.
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Tomas C, Orava M, Tuomivaara L, Martikainen H. P-064. Patients with a low fertilization rate in IVF have a low pregnancy rate in subsequent ICSI. Hum Reprod 1997. [DOI: 10.1093/humrep/12.suppl_2.150-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Martikainen H, Juntunen K, Nuojua-Huttunen S, Tuomivaara L, Tomas C. P-063. Comparison of step-down and step-up regimens in ovarian stimulation for IVF. Hum Reprod 1997. [DOI: 10.1093/humrep/12.suppl_2.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Tomas C, Nuojua-Huttunen S, Martikainen H. Pretreatment transvaginal ultrasound examination predicts ovarian responsiveness to gonadotrophins in in-vitro fertilization. Hum Reprod 1997; 12:220-3. [PMID: 9070699 DOI: 10.1093/humrep/12.2.220] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The objective of this study was to determine the predictive value of the number of follicles seen by transvaginal ultrasound before gonadotrophin stimulation on the ovarian responsiveness of 166 infertile women undergoing in-vitro fertilization (IVF) treatment. The main variables were patient age, ovarian volume and number of ovarian follicles measuring 2-5 mm on transvaginal ultrasound before gonadotrophin stimulation. Based on the sum of ovarian follicles in both ovaries the patients were divided into three groups of inactive (<5 follicles), normal (5-15 follicles) or polycystic (PCO)-like ovaries (>15 follicles). The main outcome measure was the number of recovered oocytes. The number of follicles was correlated more strongly with the number of recovered oocytes (r2 = 0.131; P = 0.0001) than age alone (r2 = -0.053; P = 0.005). Fewer oocytes were recovered from patients with inactive ovaries (5.4 +/- 2.5; P = 0.006) than with normal (7.5 +/- 4.5) or PCO-like ovaries (10.5 +/- 5.1). Ovarian volume was correlated with the number of follicles before stimulation (P = 0.0001), but not with the number of oocytes. The number of small follicles present before ovarian stimulation was a better predictor of the outcome than ovarian volume or age alone. Patients can be identified with inactive ovaries which will have a poor response to IVF treatment, a key factor for counselling couples and optimizing resources.
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Affiliation(s)
- C Tomas
- Department of Obstetrics and Gynecology, University of Oulu, Finland
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Tomas C, Risteli J, Risteli L, Stenback F, Kauppila A. Measurement of epithelial and stromal changes in vulvar carcinoma - a clinical, biochemical and immunohistochemical study. Int J Oncol 1995; 7:101-105. [PMID: 21552813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
We evaluated the clinical usefulness of the squamous cell carcinoma antigen (SCC) and CA 125, serum markers of epithelial cancer cells, in comparison with the serum concentration and tissue distribution of the aminoterminal propeptide of type III procollagen (PIIINP), a marker of connective tissue metabolism, in 31 patients with vulvar carcinoma. The SCC concentration was increased in 42%, that of CA 125 in 14% and that of PIIINP in 36% of the cases. The combination of SCC and PIIINP increased the detection rate to 57% and that of all three to 64%. None of the tumor markers correlated with the clinical stage of the disease. The initial values of the serum markers did not discriminate between different patterns of the clinical behavior of the disease. Six patients were followed with serial determinations of the markers. In each case at least one of the markers correlated with the clinical course of the disease. SCC did so in 5 cases, PIIINP in 3 cases and CA 125 in 2 cases. The mean concentrations of SCC and CA 125, but not that of PIIINP, were significantly lower during the periods of response to therapy than during the nonresponsive periods. Immunohistochemistry of PIIINP showed vulvar carcinoma to be associated with a distinct collagenous stroma. In the junctional area of the stroma around the malignant epithelium, the PIIINP positive fibers grew more sparse and irregular with decreasing differentiation of the tumor. The present data suggest that SCC, CA 125 and PIIINP are useful, especially SCC, in monitoring the clinical behaviour of the advanced vulvar cancer, less so in predicting its prognosis.
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Affiliation(s)
- C Tomas
- UNIV OULU,DEPT CLIN CHEM,SF-90220 OULU,FINLAND. UNIV OULU,DEPT MED BIOCHEM,SF-90220 OULU,FINLAND. UNIV OULU,DEPT PATHOL,SF-90220 OULU,FINLAND
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Abstract
We have irradiated abdominal cavity of 23 rats with 10 Gy irradiation-induced hypoglycemia on the fourth day after intervention. Islets collected at this time showed an impaired insulin secretion without affecting insulin content. This impairment persisted after one month follow-up with reduced number of beta-cells in morphological examination.
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Affiliation(s)
- Y Sarri
- Endocrinology and Diabetes Unit, School of Medicine, Barcelona University, Spain
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Abstract
The uptake of 3-O-[14C]methyl-D-glucose was measured in erythrocytes of normal and non-insulin-dependent diabetic subjects. In normal subjects, the uptake of the sugar was rapid, saturable, temperature-sensitive and inhibited by cytochalasin B. Over 30 s incubation at 20 degrees C, the uptake of 3-O-[14C]methyl-D-glucose (20 mM) was lower in diabetic than in normal subjects. These findings raise the view that an alteration of hexose transport into insulin-insensitive cells may participate to the perturbation of glucose homeostasis in diabetic patients.
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Affiliation(s)
- R Gomis
- Endocrinology and Diabetes Unit, Hospital Clinic, Barcelona, Spain
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