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Martínez-Barrios E, Grassi S, Brión M, Toro R, Cesar S, Cruzalegui J, Coll M, Alcalde M, Brugada R, Greco A, Ortega-Sánchez ML, Barberia E, Oliva A, Sarquella-Brugada G, Campuzano O. Molecular autopsy: Twenty years of post-mortem diagnosis in sudden cardiac death. Front Med (Lausanne) 2023; 10:1118585. [PMID: 36844202 PMCID: PMC9950119 DOI: 10.3389/fmed.2023.1118585] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
In the forensic medicine field, molecular autopsy is the post-mortem genetic analysis performed to attempt to unravel the cause of decease in cases remaining unexplained after a comprehensive forensic autopsy. This negative autopsy, classified as negative or non-conclusive, usually occurs in young population. In these cases, in which the cause of death is unascertained after a thorough autopsy, an underlying inherited arrhythmogenic syndrome is the main suspected cause of death. Next-generation sequencing allows a rapid and cost-effectives genetic analysis, identifying a rare variant classified as potentially pathogenic in up to 25% of sudden death cases in young population. The first symptom of an inherited arrhythmogenic disease may be a malignant arrhythmia, and even sudden death. Early identification of a pathogenic genetic alteration associated with an inherited arrhythmogenic syndrome may help to adopt preventive personalized measures to reduce risk of malignant arrhythmias and sudden death in the victim's relatives, at risk despite being asymptomatic. The current main challenge is a proper genetic interpretation of variants identified and useful clinical translation. The implications of this personalized translational medicine are multifaceted, requiring the dedication of a specialized team, including forensic scientists, pathologists, cardiologists, pediatric cardiologists, and geneticists.
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Affiliation(s)
- Estefanía Martínez-Barrios
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Simone Grassi
- Forensic Medical Sciences, Department of Health Science, University of Florence, Florence, Italy
| | - María Brión
- Family Heart Disease Unit, Cardiology Service, Santiago de Compostela University Hospital, Santiago de Compostela, Spain,Cardiovascular Genetics, Santiago de Compostela Health Research Institute, Santiago de Compostela, Spain,Genomic Medicine Group, Universidade de Santiago de Compostela, Santiago de Compostela, Spain,Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain
| | - Rocío Toro
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Sergi Cesar
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - José Cruzalegui
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mònica Coll
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain
| | - Mireia Alcalde
- Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain
| | - Ramon Brugada
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain,Cardiology Department, Hospital Josep Trueta, Girona, Spain
| | - Andrea Greco
- Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain,Department of Medical and Surgical Sciences of the Mother, Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - María Luisa Ortega-Sánchez
- Forensic Pathology Department, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain,School of Medicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Spain
| | - Eneko Barberia
- Forensic Pathology Department, Institut de Medicina Legal i Ciències Forenses de Catalunya (IMLCFC), Barcelona, Spain,School of Medicine and Health Sciences, Universitat Rovira i Virgili, Reus, Spain
| | - Antonio Oliva
- Section of Legal Medicine, Department of Health Surveillance and Bioethics, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Georgia Sarquella-Brugada
- Pediatric Arrhythmias, Inherited Cardiac Diseases and Sudden Death Unit, Cardiology Department, Sant Joan de Déu Hospital de Barcelona, Barcelona, Spain,European Reference Network for Rare, Low Prevalence and Complex Diseases of the Heart, Amsterdam, Netherlands,Arrítmies Pediàtriques, Cardiologia Genètica i Mort Sobtada, Malalties Cardiovasculars en el Desenvolupament, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,*Correspondence: Georgia Sarquella-Brugada,
| | - Oscar Campuzano
- Centro de Investigación Biomédica en Red en Enfermedades Cardiovasculares, Madrid, Spain,Medical Science Department, School of Medicine, University of Girona, Girona, Spain,Cardiovascular Genetics Center, Institut d’Investigacions Biomèdiques de Girona (IDIBGI), University of Girona, Girona, Spain,Oscar Campuzano,
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Eiras S, Álvarez E, Brión M, González-Juanatey JR. [COVID-19 and treatment guided by biochemical and molecular diagnostic tests to reduce myocardial damage and cardiotoxicity]. Rev Esp Cardiol 2020; 73:691-693. [PMID: 32372844 PMCID: PMC7198176 DOI: 10.1016/j.recesp.2020.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Sonia Eiras
- Grupo de Cardiología Traslacional, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, España
- Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, España
| | - Ezequiel Álvarez
- Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, España
- Grupo de Cardiología, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, España
| | - María Brión
- Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, España
- Grupo de Genética Cardiovascular, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, España
| | - José Ramón González-Juanatey
- Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, España
- Grupo de Cardiología, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, España
- Servicio de Cardiología, Hospital Clínico de Santiago de Compostela, Santiago de Compostela, A Coruña, España
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Eiras S, Álvarez E, Brión M, González-Juanatey JR. COVID-19 and treatment guided by biochemical and molecular diagnostic tests to reduce myocardial damage and cardiotoxicity. Rev Esp Cardiol (Engl Ed) 2020; 73:691-693. [PMID: 32493574 PMCID: PMC7245328 DOI: 10.1016/j.rec.2020.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 04/27/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Sonia Eiras
- Grupo de Cardiología Traslacional, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, Spain; Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, Spain
| | - Ezequiel Álvarez
- Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, Spain; Grupo de Cardiología, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, Spain
| | - María Brión
- Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, Spain; Grupo de Genética Cardiovascular, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, Spain
| | - José Ramón González-Juanatey
- Centro de Investigación Biomédica en Red Enfermedades Cardiovaculares, CIBERCV, Madrid, Spain; Grupo de Cardiología, Instituto de Investigación Sanitaria, Santiago de Compostela, A Coruña, Spain; Servicio de Cardiología, Hospital Clínico de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain.
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Grassi S, Campuzano O, Coll M, Brión M, Arena V, Iglesias A, Carracedo Á, Brugada R, Oliva A. Genetic variants of uncertain significance: How to match scientific rigour and standard of proof in sudden cardiac death? Leg Med (Tokyo) 2020; 45:101712. [PMID: 32361481 DOI: 10.1016/j.legalmed.2020.101712] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 07/05/2019] [Revised: 02/17/2020] [Accepted: 04/21/2020] [Indexed: 02/08/2023]
Abstract
In many SCD cases, in particular in pediatric age, autopsy can be completely negative and then a post-mortem genetic testing (molecular autopsy) is indicated. In NGS era finding new/rare variants is extremely frequent and, when only variants of unknown significance are found, molecular autopsy fails to find a cause of death. We describe the emblematic case of the sudden death of a 7-year-old girl. We performed a full-body micro-CT analysis, an accurate autopsy, a serum tryptase test and toxicological tests. Since the only macroscopic abnormality we found was a myocardial bridging (length: 1,1 cm, thickness: 0,5 cm) of the left anterior descending coronary artery, a molecular autopsy has been performed. NGS analysis on victim DNA detected rare variants in DPP6, MYH7, SCN2B and NOTCH1 and segregation analysis was then achieved. On the basis of ACMG/AMP (clinical) guidelines, all the found variants were classified as of unknown significance. In other words, both the macroscopic and genetic anomalies we found were of uncertain significance and then the autopsy failed to find the cause of the death. Our case raises three main discussion points: (a) economical, ethical and legal limitations of genetic investigation; (b) risk that genetic testing does not succeed in finding a certain cause of the death; (c) absence of specific guidelines to face the problem of VUS in forensic cases.
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Affiliation(s)
- Simone Grassi
- Institute of Public Health, Section of Legal Medicine, Catholic University, Rome, Italy
| | - Oscar Campuzano
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain; Medical Science Department, School of Medicine, University of Girona, Girona, Spain; Centro Investigación Biomédica Red Enfermedades Cardiovasculares, Madrid, Spain; Department of Biochemistry and Molecular Genetics, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Mònica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - María Brión
- Genetics of Cardiovascular and Ophthalmological Diseases, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Genomic Medicine, University of Santiago de Compostela, IDIS, CIBERER, Santiago de Compostela, Spain
| | - Vincenzo Arena
- Institute of Anatomical Pathology, Catholic University, Rome, Italy
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Ángel Carracedo
- Genomic Medicine, University of Santiago de Compostela, IDIS, CIBERER, Santiago de Compostela, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain; Medical Science Department, School of Medicine, University of Girona, Girona, Spain; Centro Investigación Biomédica Red Enfermedades Cardiovasculares, Madrid, Spain; Cardiology Service, Hospital Josep Trueta, Girona, Spain
| | - Antonio Oliva
- Institute of Public Health, Section of Legal Medicine, Catholic University, Rome, Italy.
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Brión M, de Castro López MJ, Santori M, Pérez Muñuzuri A, López Abel B, Baña Souto AM, Martínez Soto MI, Couce ML. Prospective and Retrospective Diagnosis of Barth Syndrome Aided by Next-Generation Sequencing. Am J Clin Pathol 2016; 145:507-13. [PMID: 27124939 DOI: 10.1093/ajcp/aqw025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To establish a genetic and clinical diagnosis in a newborn with fetal-onset dilated cardiomyopathy using next-generation sequencing technologies. METHODS We have conducted the clinical evaluation of the proband and the molecular characterization of his disease by means of whole-exome sequencing. In addition, the clinical evaluation and subsequent genetic screening of five relatives has been performed. This comprises two males with features of left ventricular noncompaction cardiomyopathy, two females suspected of being carriers, and one pregnant female at risk of being a carrier and thereby transmitting the disease to her child. RESULTS We have discovered a novel variant in the TAZ gene by means of whole-exome sequencing. This, together with the performance of further clinical analyses, led to an early diagnosis of Barth syndrome in the proband. The genetic screening of the subject's familial group revealed full cosegregation of the variant with another two affected males and identified several female carriers. CONCLUSIONS The investigation for Barth syndrome must be considered in male babies and young boys with dilated cardiomyopathy and left ventricular noncompaction. Next-generation sequencing technologies provide an accurate and rapid diagnostic tool in prospectively and retrospectively identifying individuals with this Mendelian syndrome.
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Affiliation(s)
- María Brión
- From the Grupo de Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular, Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | | | - Montserrat Santori
- From the Grupo de Xenética de Enfermidades Cardiovasculares, Instituto de Investigación Sanitaria de Santiago, Red de Investigación Cardiovascular, Fundación Pública Galega de Medicina Xenómica, SERGAS, Santiago de Compostela, Spain
| | | | - Bernardo López Abel
- Pediatric Cardiac Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - María Isabel Martínez Soto
- Pediatric Cardiac Unit, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
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Suárez-Rama JJ, Arrojo M, Sobrino B, Amigo J, Brenlla J, Agra S, Paz E, Brión M, Carracedo Á, Páramo M, Costas J. Resequencing and association analysis of coding regions at twenty candidate genes suggest a role for rare risk variation at AKAP9 and protective variation at NRXN1 in schizophrenia susceptibility. J Psychiatr Res 2015; 66-67:38-44. [PMID: 25943950 DOI: 10.1016/j.jpsychires.2015.04.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/10/2015] [Accepted: 04/14/2015] [Indexed: 12/20/2022]
Abstract
A fraction of genetic risk to develop schizophrenia may be due to low-frequency variants. This multistep study attempted to find low-frequency variants of high effect at coding regions of eleven schizophrenia susceptibility genes supported by genome-wide association studies (GWAS) and nine genes for the DISC1 interactome, a susceptibility gene-set. During the discovery step, a total of 125 kb per sample were resequenced in 153 schizophrenia patients and 153 controls from Galicia (NW Spain), and the cumulative role of low-frequency variants at a gene or at the DISC1 gene-set were analyzed by burden and variance-based tests. Relevant results were meta-analyzed when appropriate data were available. In addition, case-only putative damaging variants were genotyped in a further 419 cases and 398 controls. The discovery step revealed a protective effect of rare missense variants at NRXN1, a result supported by meta-analysis (OR = 0.67, 95% CI: 0.47-0.94, P = 0.021, based on 3848 patients and 3896 controls from six studies). The follow-up step based on case-only putative damaging variants revealed a promising risk variant at AKAP9. This variant, K873R, reached nominal significance after inclusion of 240 additional Spanish controls from databases. The variant, located in an ADCY2 binding region, is absent from large public databases. Interestingly, GWAS revealed an association between common ADCY2 variants and bipolar disorder, a disorder with considerable genetic overlap with schizophrenia. These data suggest a role of rare missense variants at NRXN1 and AKAP9 in schizophrenia susceptibility, probably related to alteration of the excitatory/inhibitory synaptic balance, deserving further investigation.
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Affiliation(s)
- José Javier Suárez-Rama
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Arrojo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Beatriz Sobrino
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Jorge Amigo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Julio Brenlla
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago(CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Santiago Agra
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago(CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Eduardo Paz
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago(CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - María Brión
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Ángel Carracedo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Mario Páramo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago(CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Javier Costas
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Spain.
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Ramos-Luis E, Blanco-Verea A, Brión M, Van Huffel V, Sánchez-Diz P, Carracedo A. Y-chromosomal DNA analysis in French male lineages. Forensic Sci Int Genet 2013; 9:162-8. [PMID: 24528594 DOI: 10.1016/j.fsigen.2013.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 07/29/2013] [Revised: 12/16/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
Abstract
French population, despite of its crucial geographic location for repopulation movements of Europe across time, it has been insufficiently characterized at the genetic level, especially for Y-chromosomal DNA variation. In order to make a genetic structure characterization, we have analyzed the Y-chromosome diversity of 558 male individuals, scattered along 7 different French regions: Alsace (Strasbourg), Auvergne (Clermont-Ferrand), Bretagne (Rennes), Île-de-France (Paris), Midi-Pyrénées (Toulouse), Nord-Pas-de-Calais (Lille) and Provence-Alpes-Côte d'Azur (Marseille). A total of 17 Y-chromosome STRs and 27 Y-chromosome SNPs were genotyped for each individual. Even though we find that most of the individual populations in France were not differentiated from each other, Bretagne population shows population substructure, an important fact to be considered when establishing general population databases.
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Affiliation(s)
- E Ramos-Luis
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain.
| | - A Blanco-Verea
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - M Brión
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - V Van Huffel
- Institut National de la Transfusion Sanguine, Paris, France
| | - P Sánchez-Diz
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - A Carracedo
- Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
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Corton M, Avila-Fernandez A, Vallespín E, López-Molina MI, Almoguera B, Martín-Garrido E, Tatu SD, Khan MI, Blanco-Kelly F, Riveiro-Alvarez R, Brión M, García-Sandoval B, Cremers FPM, Carracedo A, Ayuso C. Involvement of LCA5 in Leber congenital amaurosis and retinitis pigmentosa in the Spanish population. Ophthalmology 2013; 121:399-407. [PMID: 24144451 DOI: 10.1016/j.ophtha.2013.08.028] [Citation(s) in RCA: 11] [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: 06/10/2013] [Revised: 07/29/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVE We aimed to identify novel genetic defects in the LCA5 gene underlying Leber congenital amaurosis (LCA) in the Spanish population and to describe the associated phenotype. DESIGN Case series. PARTICIPANTS A cohort of 217 unrelated Spanish families affected by autosomal recessive or isolated retinal dystrophy, that is, 79 families with LCA and 138 families with early-onset retinitis pigmentosa (EORP). A total of 100 healthy, unrelated Spanish individuals were screened as controls. METHODS High-resolution homozygosity mapping was performed in 44 patients with LCA using genome-wide single nucleotide polymorphism (SNP) microarrays. Direct sequencing of the LCA5 gene was performed in 5 patients who showed homozygous regions at chromosome 6 and in 173 unrelated individuals with LCA or EORP. The ophthalmic history of 8 patients carrying LCA5 mutations was reviewed and additional examinations were performed, including electroretinography (ERG), optical coherence tomography (OCT), and fundus photography. MAIN OUTCOME MEASURES Single nucleotide polymorphism genotyping, identity-by-descent (IBD) regions, LCA5 mutations, best-corrected visual acuity, visual field assessments, fundus appearance, ERG, and OCT findings. RESULTS Four novel and 2 previously reported LCA5 mutations have been identified in 6 unrelated families with LCA by homozygosity mapping or Sanger sequencing. Thus, LCA5 mutations have a frequency of 7.6% in the Spanish population. However, no LCA5 mutations were found in 138 patients with EORP. Although most of the identified LCA5 mutations led to a truncated protein, a likely pathogenic missense variant was identified for the first time as a cause of LCA, segregating in 2 families. We also have characterized a novel splicing site mutation at the RNA level, demonstrating that the mutant LCA5 transcript was absent in a patient. All patients carrying LCA5 mutations presented nystagmus, night blindness, and progressive loss of visual acuity and visual field leading to blindness toward the third decade of life. Fundoscopy showed fundus features of pigmentary retinopathy with atrophic macular lesions. CONCLUSIONS This work reveals a higher frequency of LCA5 mutations in a Spanish LCA cohort than in other populations. This study established gene-specific frequencies and the underlying phenotype of LCA5 mutations in the Spanish population.
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Affiliation(s)
- Marta Corton
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Elena Vallespín
- Instituto de Genética Médica y Molecular, IdiPaz, Hospital Universitario La Paz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - María Isabel López-Molina
- Department of Ophthalmology, Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Berta Almoguera
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Esther Martín-Garrido
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Sorina D Tatu
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - M Imran Khan
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Fiona Blanco-Kelly
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - María Brión
- Genetics of Cardiovascular and Ophthalmologic Diseases, Instituto de Investigación Sanitaria de Santiago de Compostela, RIC, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Blanca García-Sandoval
- Department of Ophthalmology, Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Angel Carracedo
- Genomic Medicine Group-USC, Fundación Publica Galega de Medicina Xenómica, Santiago de Compostela, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain
| | - Carmen Ayuso
- Department of Genetics, IIS - Fundación Jiménez Díaz, Madrid, Spain; Centre for Biomedical Network Research on Rare Diseases, ISCIII, Valencia, Spain.
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9
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Brión M, Sanchez-Salorio M, Cortón M, de la Fuente M, Pazos B, Othman M, Swaroop A, Abecasis G, Sobrino B, Carracedo A. Genetic association study of age-related macular degeneration in the Spanish population. Acta Ophthalmol 2011; 89:e12-22. [PMID: 21106043 DOI: 10.1111/j.1755-3768.2010.02040.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
PURPOSE To investigate new genetic risk factors and replicate reported associations with advanced age-related macular degeneration (AMD) in a prospective case-control study developed with a Spanish cohort. METHODS Three hundred and fifty-three unrelated patients with advanced AMD (225 with atrophic AMD, 57 with neovascular AMD, and 71 with mixed AMD) and 282 age-matched controls were included. Functional and tagging SNPs in 55 candidate genes were genotyped using the SNPlex™ genotyping system. Single SNP and haplotype association analysis were performed to determine possible genetic associations; interaction effects between SNPs were also investigated. RESULTS In agreement with previous reports, ARMS2 and CFH genes were strongly associated with AMD in the studied Spanish population. Moreover, both loci influenced risk independently giving support to different pathways implicated in AMD pathogenesis. No evidence for association of advanced AMD with other previous reported susceptibility genes, such as CST3, CX3CR1, FBLN5, HMCN1, PON1, SOD2, TLR4, VEGF and VLDLR, was detected. However, two additional genes appear to be candidate markers for the development of advanced AMD. A variant located at the 3' UTR of the FGF2 gene (rs6820411) was highly associated with atrophic AMD, and the functional SNP rs3112831 at ABCA4 showed a marginal association with the disease. CONCLUSION We performed a large gene association study in advanced AMD in a Spanish population. Our findings show that CFH and ARMS2 genes seem to be the principal risk loci contributing independently to AMD in our cohort. We report new significant associations that could also influence the development of advanced AMD. These findings should be confirmed in further studies with larger cohorts.
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Affiliation(s)
- María Brión
- Hospital-University Complex of Santiago, Santiago de Compostela, Spain.
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10
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Blanco-Verea A, Jaime JC, Brión M, Carracedo A. Y-chromosome lineages in native South American population. Forensic Sci Int Genet 2009; 4:187-93. [PMID: 20215030 DOI: 10.1016/j.fsigen.2009.08.008] [Citation(s) in RCA: 19] [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: 04/27/2009] [Revised: 07/31/2009] [Accepted: 08/16/2009] [Indexed: 10/20/2022]
Abstract
The present work tries to investigate the population structure and variation of the Amerindian indigenous populations living in Argentina. A total of 134 individuals from three ethnic groups (Kolla, Mapuche and Diaguitas) living in four different regions were collected and analysed for 26 Y-SNPs and 11 Y-STRs. Intra-population variability was analysed, looking for population substructure and neighbour populations were considered for genetic comparative analysis, in order to estimate the contribution of the Amerindian and the European pool, to the current population. We observe a high frequency of R1b1 and Q1a3a* Y-chromosome haplogroups, in the ethnic groups Mapuche, Diaguita and Kolla, characteristic of European and Native American populations, respectively. When we compare our native Argentinean population with other from the South America we also observe that frequency values for Amerindian lineages are relatively lower in our population. These results show a clear Amerindian genetic component but we observe a predominant European influence too, suggesting that typically European male lineages have given rise to the displacement of genuinely Amerindian male lineages in our South American population.
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Affiliation(s)
- A Blanco-Verea
- Complexo Hospitalario Universitario de Santiago (CHUS), Santiago de Compostela, Spain.
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11
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Blanco-Verea A, Brión M, Ramos-Luis E, Lareu M, Carracedo A. Forensic validation and implementation of Y-chromosome SNP multiplexes. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.046] [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: 10/22/2022]
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12
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Lovo-Gómez J, Blanco-Verea A, Lareu MV, Brión M, Carracedo A. The genetic male legacy from El Salvador. Forensic Sci Int 2007; 171:198-203. [PMID: 16916590 DOI: 10.1016/j.forsciint.2006.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 07/05/2006] [Accepted: 07/06/2006] [Indexed: 12/01/2022]
Abstract
Allele frequencies and haplotype and haplogroup analysis have been performed for 16 Y-chromosome binary markers and 8 Y-chromosome STRs (DYS19, DYS385I and II, DYS389I and II, DYS390, DYS391, DYS392, DYS393). Data was obtained from a general sample of 93 unrelated individuals living in metropolitan areas from El Salvador, and 67 individuals from different historical ethnic groups, Conchagua, San Alejo, Panchimalco, Izalco and finally Nueva Concepción with white people. Levels of admixture among metropolitan and rural areas were evaluated and population substructure measured. A total of 13 haplogroups and 136 different haplotypes were found. The most frequent haplogroup in the general metropolitan population was the European R1b, while in the Indigenous samples considered as a whole the most frequent was the Amerindian haplogroup Q3.
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Affiliation(s)
- J Lovo-Gómez
- Laboratorio de Genética Forense, Instituto de Medicina Legal Dr. Roberto Masferrer, Corte Suprema de Justicia, San Salvador, El Salvador
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13
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Brión M, Sanchez J, Balogh K, Thacker C, Blanco-Verea A, Børsting C, Stradmann-Bellinghausen B, Bogus M, Syndercombe-Court D, Schneider P, Carracedo A, Morling N. Analysis of 29 Y-chromosome SNPs in a single multiplex useful to predict the geographic origin of male lineages. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.ics.2005.09.140] [Citation(s) in RCA: 3] [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: 10/24/2022]
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14
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Brión M, Sanchez JJ, Balogh K, Thacker C, Blanco-Verea A, Børsting C, Stradmann-Bellinghausen B, Bogus M, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N. Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages. Electrophoresis 2006; 26:4411-20. [PMID: 16273584 DOI: 10.1002/elps.200500293] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [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: 11/09/2022]
Abstract
The European Consortium "High-throughput analysis of single nucleotide polymorphisms for the forensic identification of persons--SNPforID", has performed a selection of candidate Y-chromosome single nucleotide polymorphisms (SNPs) for making inferences on the geographic origin of an unknown sample. From more than 200 SNPs compiled in the phylogenetic tree published by the Y-Chromosome Consortium, and looking at the population studies previously published, a package of 29 SNPs has been selected for the identification of major population haplogroups. A "Major Y-chromosome haplogroup typing kit" has been developed, which allows the multiplex amplification of all 29 SNPs in a single reaction. Allele genotyping was performed with a single base extension reaction (minisequencing) detected by CE. The validation of the multiplex was performed in a total of 1126 unrelated males distributed among 12 worldwide populations. The approach takes advantage of the specific geographic distribution of the Y-chromosome haplogroups and demonstrates the utility of binary polymorphisms to infer the origin of a male lineage.
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Affiliation(s)
- María Brión
- Institute of Legal Medicine, National Genotyping Center (CEGEN), University of Santiago de Compostela, Spain.
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15
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Palacio OD, Triana O, Gaviria A, Ibarra AA, Ochoa LM, Posada Y, Maya MC, Lareu MV, Brión M, Acosta MA, Carracedo A. Autosomal microsatellite data from Northwestern Colombia. Forensic Sci Int 2005; 160:217-20. [PMID: 16024199 DOI: 10.1016/j.forsciint.2005.05.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 05/25/2005] [Accepted: 05/25/2005] [Indexed: 11/23/2022]
Abstract
Allele frequencies and some forensic parameters for 12 autosomal microsatellites (CSF1PO, TPOX, THO1, VWA, D16S539, D7S820, D13S317, D5S818, F13A1, FESFPS, F13B, LPL) were estimated from three departments from Northwestern Colombia. The total number of samples analysed was 1045 individuals. Comparative analysis among the three studied departments and with other published Colombian populations were also performed and discussed.
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Affiliation(s)
- Oscar Darío Palacio
- Institute of Biology, Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia
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16
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Lovo JS, Fondevila M, Salas A, Brión M, Lareu MV, Carracedo Á. Corrigendum to “Y-chromosome STR-haplotype typing in EI Salvador [Forensic Sci. Int. 142 (1) (2004) 45–49]”. Forensic Sci Int 2005. [DOI: 10.1016/j.forsciint.2005.01.003] [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: 10/25/2022]
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17
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Abstract
Single nucleotide polymorphisms (SNPs) are the most frequent polymorphisms described in the human genome, and their analysis is becoming an extensive routine in molecular biology, not only in the forensic field, but also in population and clinical genetics. In particular, SNPs located on the Y chromosome have a specific utility as forensic tools, and based on this fact, we have designed a strategy that allows us to identify the most frequent haplogroups in European populations. We selected 29 markers among the 245 binary polymorphisms described in the Y-Chromosome Consortium tree. The whole set was grouped into four multiplexes in a hierarchical way, allowing us to determine the final haplogroup using only one or two multiplexes. In this way, we only type in the best-case nine SNPs, and in the worst possible combination 17 SNPs, to define the haplogroup. The selected strategy to type the SNPs was a single-base extension method using the SNaPshot multiplex kit from Applied Biosystems, and detailed practical procedures are described here. With this hierarchical strategy adapted for European populations the massive typing of SNPs was avoided, and therefore the time and money involved in the study was also reduced.
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Affiliation(s)
- María Brión
- Institute of Legal Medicine, Faculty of Medicine, University of Santiago de Compostela, Santiago de Compostela, Galicia, Spain
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18
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Sobrino B, Brión M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int 2005; 154:181-94. [PMID: 16182964 DOI: 10.1016/j.forsciint.2004.10.020] [Citation(s) in RCA: 292] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 10/10/2004] [Accepted: 10/15/2004] [Indexed: 11/22/2022]
Abstract
There is an increasing interest in single nucleotide polymorphism (SNP) typing in the forensic field, not only for the usefulness of SNPs for defining Y chromosome or mtDNA haplogroups or for analyzing the geographical origin of samples, but also for the potential applications of autosomal SNPs. The interest of forensic researchers in autosomal SNPs has been attracted due to the potential advantages in paternity testing because of the low mutation rates and specially in the analysis of degraded samples by use of short amplicons. New SNP genotyping methods, chemistries and platforms are continuously being developed and it is often difficult to be keeping up to date and to decide on the best technology options available. This review offers to the reader a state of the art of SNP genotyping technologies with the advantages and disadvantages of the different chemistries and platforms for different forensic requirements.
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Affiliation(s)
- Beatriz Sobrino
- Institute of Legal Medicine, University of Santiago de Compostela, San Francisco s/n, Spain.
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19
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Gaviria AA, Ibarra AA, Palacio OD, Posada YC, Triana O, Ochoa LM, Acosta MA, Brión M, Lareu MV, Carracedo A. Y-chromosome haplotype analysis in Antioquia (Colombia). Forensic Sci Int 2004; 151:85-91. [PMID: 15935946 DOI: 10.1016/j.forsciint.2004.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2003] [Revised: 07/13/2004] [Accepted: 07/15/2004] [Indexed: 10/26/2022]
Abstract
Allele frequencies and haplotype analysis have been performed for eight Y-chromosome STRs (DYS19, DYS385 I and II, DYS389 I and II, DYS390, DYS391, DYS392, DYS393). Population data was obtained from a sample of 400 unrelated individuals living in Antioquia (Colombia). A total of 270 different haplotypes were found, and the haplotype diversity was 0.989. The first and second most frequent haplotypes where shared by 8 and 6% of the individuals, respectively.
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Affiliation(s)
- A A Gaviria
- Forensic Genetics, Biology Department, Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia.
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20
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Lovo JS, Saul J, Fondevila M, Salas A, Brión M, Lareu MV, Carracedo A. Y-chromosome STR-haplotype typing in El Salvador. Forensic Sci Int 2004; 142:45-9. [PMID: 15110073 DOI: 10.1016/j.forsciint.2004.02.004] [Citation(s) in RCA: 10] [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] [Received: 02/08/2004] [Accepted: 02/09/2004] [Indexed: 11/27/2022]
Abstract
Eight Y-chromosome STRs were investigated in a male population sample from El Salvador. Complete Y-chromosomal STRs haplotypes were obtained in 121 individuals, among which 107 different haplotypes were observed. The two most common haplotypes were shared by approximately 4% of the sample, while 100 haplotypes were unique. The gene diversity was 0.9883 and the discrimination capacity was 0.8926. The combined Y-chromosome STR polymorphisms provide a powerful discrimination tool for routine forensic applications.
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Affiliation(s)
- José Saul Lovo
- Facultad de Medicina, Instituto de Medicina Legal, University of Santiago de Compostela, C/San Francisco s/n, 15782 Santiago de Compostela, Galicia, Spain
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21
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Brión M, Cao R, Salas A, Lareu MV, Carracedo A. New method to measure minisatellite variant repeat variation in population genetic studies. Am J Hum Biol 2002; 14:421-8. [PMID: 12112563 DOI: 10.1002/ajhb.10057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [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: 11/10/2022] Open
Abstract
The classical analysis of minisatellite variant repeat (MVR) variation using modular structures is limited by the lack of knowledge of the mutational process involved in the evolution of most of the minisatellites. In this study a new method to measure MVR variation and to calculate genetic distances using MVR codes is proposed. The method is based on the statistical similarity of MVR patterns and considers the complete variability of the minisatellite, enabling meaningful comparisons of closely related populations. As an example, the method has been applied to analyze variation in MSY1 (DYF155S1) in five sets of data from European and North African populations.
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Affiliation(s)
- M Brión
- Institute of Legal Medicine, University of Santiago de Compostela, E-15705 Santiago de Compostela, Galicia, Spain
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22
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Sánchez-Diz P, Lareu MV, Brión M, Skitsa I, Carracedo A. STR data for the AmpFlSTR Profiler Plus loci from Greece. Forensic Sci Int 2002; 126:265-6. [PMID: 12380573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Allele frequencies for the nine STRs included in the AmpFlSTR Profiler Plus kit (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) were estimated from a sample of 143 unrelated individuals living in different regions of Greece.
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Affiliation(s)
- Paula Sánchez-Diz
- Faculty of Medicine, Institute of Legal Medicine, University of Santiago de Compostela, C/ San Francisco s/n, Spain
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23
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Abstract
A novel methodology based on PCR monitoring on-line with fluorescent formats using the LightCycler for Y chromosome SNP typing is proposed. The main advantages of the system are the time necessary for the analysis (which is around 20 min), the robustness and the accuracy of the method and especially its sensitivity, which permits the detection of the male component in male-female mixtures up to 1:300 for some of the SNPs. Singleplexes of four different SNPs (M9, sY81, SRY-1532 and SRY-2627) as well as two duplexes (M9 and sY81 on the one hand and SRY-1532 and SRY-2627 on the other) were efficiently implemented. A simultaneous amplification and analysis of the four SNPs is also possible. It seems difficult with the current methodology to implement more than a quadruplex.
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Affiliation(s)
- M Lareu
- Institute of Legal Medicine, University of Santiago de Compostela, E-15705 Santiago de Compostela, Galicia, Spain.
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24
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Pereira L, Prata MJ, Brión M, Jobling MA, Carracedo A, Amorim A. Clinal variation of YAP+ Y-chromosome frequencies in Western Iberia. Hum Biol 2000; 72:937-44. [PMID: 11236865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The potential of Y-chromosome biallelic marker haplotypes to infer population affiliations and structures was exploited to analyze four populations from the southwestern edge of Europe, namely north, central, and south Portugal and Galicia. Three markers subdividing the YAP+ lineage were analyzed: the YAP Alu element insertion itself and the SRY8299 and sY81 base substitutions; these respectively define three haplotypes known as 4, 21, and 8. Only haplotype 21 was detected presenting an increasing north-to-south frequency gradient, from 9.6% (Galicia) to 24.5% (South Portugal). This clinal distribution most likely reflects the genetic input associated with the Neolithic spread of agriculture, but we cannot exclude other movements as potential contributors to the distribution. In this context, it is interesting to note the consistency between the clinal variation and the population movement associated with Islamic rule in Iberia. The absence of haplotype 8, a marker of sub-Saharan populations, suggests that, despite the massive introductions of African slaves in historical times, there was little admixture between the African males and Western Iberian populations.
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Affiliation(s)
- L Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
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25
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Abstract
Seven Y-specific STR loci (DYS19, DYS389I, DY5389II, DYS390, DYS391, DYS392 and DYS393) were studied in five populations from the Iberian Peninsula: Andalusia, Valencia, Basque Country, Galicia and Northern Portugal. Haplotype and allele frequencies of these seven Y-chromosome STRs were estimated. Observed haplotype diversities are in a range between 0.96 (Basque Country) and 0.99 (Valencia and Andalusia). Significant population differentiation was registered between Basques and all the other Iberian populations and also between Valencia and Northern Portugal.
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Affiliation(s)
- A González-Neira
- Institute of Legal Medicine, University of Santiago de Compostela, E-15705 Santiago de Compostela, Galicia, Spain
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26
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Gusmão L, González-Neira A, Pestoni C, Brión M, Lareu MV, Carracedo A. Robustness of the Y STRs DYS19, DYS389 I and II, DYS390 and DYS393: optimization of a PCR pentaplex. Forensic Sci Int 1999; 106:163-72. [PMID: 10680065 DOI: 10.1016/s0379-0738(99)00187-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [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: 11/17/2022]
Abstract
Various technical methods were investigated with the aim of developing a multiplex system to amplify five Y-chromosome STR loci in the same PCR reaction: DYS393, DYS19, DYS390, DYS389 I and DYS389 II. A sequenced allelic ladder was constructed with previously sequenced alleles including the most common ones. A number of reamplification conditions of the allelic ladders were tested. The pentaplex was evaluated for typing using two different platforms (ABI and ALF) with promising results. However, in degraded samples non-specific artifacts were observed in the DYS393 system in the same range of sizes as the real alleles. This system can also be typed in females under relatively low stringency conditions in the PCR amplification, making this system prone to errors in critical samples. This lack of specificity can be reduced by increasing the stringency of the PCR conditions. The DYS19 ladder cannot be reamplified as stutters appear after a few reamplifications. These stutters are probably due to a 2 bp slippage induced by the presence of a TA repeat stretch in the PCR amplified fragments. Non-specific products were also noted in the DYS389 I and DYS389 II amplification, although out of the range of other alleles in this pentaplex. This newly constructed pentaplex has proved to be very useful in population genetic studies because all five Y STR markers can be loaded in the same lane of a gel with other Y STR singleplex or multiplexes. The usefulness of Y-chromosome STRs in criminal casework is especially evident in analyzing azoospermic individuals.
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Affiliation(s)
- L Gusmão
- Institute of Legal Medicine, University of Santiago de Compostela, Galicia, Spain
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