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Bernini Di Michele A, Onofri V, Pesaresi M, Turchi C. The Role of miRNA Expression Profile in Sudden Cardiac Death Cases. Genes (Basel) 2023; 14:1954. [PMID: 37895303 PMCID: PMC10606010 DOI: 10.3390/genes14101954] [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: 09/06/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Sudden cardiac death (SCD) is one of the leading causes of death in the world and for this reason it has attracted the attention of numerous researchers in the field of legal medicine. It is not easy to determine the cause in a SCD case and the available methods used for diagnosis cannot always give an exhaustive answer. In addition, the molecular analysis of genes does not lead to a clear conclusion, but it could be interesting to focus attention on the expression level of miRNAs, a class of non-coding RNA of about 22 nucleotides. The role of miRNAs is to regulate the gene expression through complementary binding to 3'-untraslated regions of miRNAs, leading to the inhibition of translation or to mRNA degradation. In recent years, several studies were performed with the aim of exploring the use of these molecules as biomarkers for SCD cases, and to also distinguish the causes that lead to cardiac death. In this review, we summarize experiments, evidence, and results of different studies on the implication of miRNAs in SCD cases. We discuss the different biological starting materials with their respective advantages and disadvantages, studying miRNA expression on tissue (fresh-frozen tissue and FFPE tissue), circulating cell-free miRNAs in blood of patients affected by cardiac disease at high risk of SCD, and exosomal miRNAs analyzed from serum of people who died from SCD.
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Affiliation(s)
- Alessia Bernini Di Michele
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto, 60126 Ancona, Italy; (A.B.D.M.); (M.P.)
| | - Valerio Onofri
- Legal Medicine Unit, AOU Azienda Ospedaliero Universitaria delle Marche, 60126 Ancona, Italy;
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto, 60126 Ancona, Italy; (A.B.D.M.); (M.P.)
| | - Chiara Turchi
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto, 60126 Ancona, Italy; (A.B.D.M.); (M.P.)
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Turchi C, Melchionda F, Alessandrini F, Onofri V, Pesaresi M, Buscemi L, Tagliabracci A. Pitfalls, challenges and caveats in whole mitochondrial genome sequencing from hair shafts by MPS: Where, when and how to address them. Forensic Science International: Genetics Supplement Series 2022. [DOI: 10.1016/j.fsigss.2022.10.041] [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: 12/23/2022]
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Turchi C, Previderè C, Bini C, Carnevali E, Grignani P, Manfredi A, Melchionda F, Onofri V, Pelotti S, Robino C, Sorçaburu-Ciglieri S, Tagliabracci A, Fattorini P. Assessment of the Precision ID Identity Panel kit on challenging forensic samples. Forensic Sci Int Genet 2020; 49:102400. [DOI: 10.1016/j.fsigen.2020.102400] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/28/2020] [Accepted: 09/25/2020] [Indexed: 12/18/2022]
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Alessandrini F, Caucci S, Onofri V, Melchionda F, Tagliabracci A, Bagnarelli P, Di Sante L, Turchi C, Menzo S. Evaluation of the Ion AmpliSeq SARS-CoV-2 Research Panel by Massive Parallel Sequencing. Genes (Basel) 2020; 11:E929. [PMID: 32806776 PMCID: PMC7463572 DOI: 10.3390/genes11080929] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion AmpliSeq™ SARS-CoV-2 Research Panel by a massively parallel sequencing (MPS) assay. The panel allows for targeted sequencing by overlapping amplicons, thereby providing specific, accurate, and high throughput analysis. A modified reverse transcription reaction, which consists of the use of a SARS-CoV-2 specific primers pool from the Ion AmpliSeq SARS-CoV-2 Research Panel, was assessed in order to promote viral RNA specific reverse transcription. The aim of this study was to evaluate the effectiveness of the Ion AmpliSeq™ SARS-CoV-2 Research Panel in sequencing the entire viral genome in different samples. SARS-CoV-2 sequence data were obtained from ten viral isolates and one nasopharyngeal swab from different patients. The ten isolate samples amplified with 12 PCR cycles displayed high mean depth values compared to those of the two isolates amplified with 20 PCR cycles. High mean depth values were also obtained for the nasopharyngeal swab processed by use of a target-specific reverse transcription. The relative depth of coverage (rDoC) analysis showed that when 12 PCR cycles were used, all target regions were amplified with high sequencing coverage, while in libraries amplified at 20 cycles, a poor uniformity of amplification, with absent or low coverage of many target regions, was observed. Our results show that the Ion AmpliSeq SARS-CoV-2 Research Panel can achieve rapid and high throughput SARS-CoV-2 whole genome sequencing from 10 ng of DNA-free viral RNA from isolates and from 1 ng of DNA-free viral RNA from a nasopharyngeal swab using 12 PCR cycles for library amplification. The modified RT-PCR protocol yielded superior results on the nasopharyngeal swab compared to the reverse transcription reaction set up according to the manufacturer's instructions.
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Affiliation(s)
- Federica Alessandrini
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Valerio Onofri
- Legal Medicine Unit, AOU Ospedali Riuniti, Torrette, 60126 Ancona, Italy;
| | - Filomena Melchionda
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Adriano Tagliabracci
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Patrizia Bagnarelli
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Laura Di Sante
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Chiara Turchi
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
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Robino C, Ralf A, Pasino S, De Marchi MR, Ballantyne KN, Barbaro A, Bini C, Carnevali E, Casarino L, Di Gaetano C, Fabbri M, Ferri G, Giardina E, Gonzalez A, Matullo G, Nutini AL, Onofri V, Piccinini A, Piglionica M, Ponzano E, Previderè C, Resta N, Scarnicci F, Seidita G, Sorçaburu-Cigliero S, Turrina S, Verzeletti A, Kayser M. Corrigendum to "Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise" [Forensic. Sci. Int. Genet. 15 (2015) 56-63]. Forensic Sci Int Genet 2018; 34:e23-e24. [PMID: 29428588 DOI: 10.1016/j.fsigen.2018.01.008] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- C Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy.
| | - A Ralf
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - S Pasino
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - M R De Marchi
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - K N Ballantyne
- Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Australia
| | - A Barbaro
- Department of Forensic Genetics, Studio Indagini Mediche e Forensi (SIMEF), Reggio Calabria, Italy
| | - C Bini
- Department of Medical and Surgical Sciences, Institute of Legal Medicine, University of Bologna, Italy
| | - E Carnevali
- Department of Biomedical and Surgical Sciences, Section of Legal Medicine and Forensic Science, University of Perugia, Italy
| | - L Casarino
- Dipartimento di Medicina Legale, del Lavoro, Psicologia Medica e Criminologia, Università di Genova, Italy
| | - C Di Gaetano
- Department of Medical Sciences, University of Turin, Italy; HuGeF, Human Genetics Foundation, Turin, Italy
| | - M Fabbri
- Department of Public Health, UOL of Legal Medicine, University of Ferrara, Italy
| | - G Ferri
- SC Medicina Legale, Università di Modena, Italy
| | - E Giardina
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Italy
| | - A Gonzalez
- ANDROS Day Surgery Clinic, Forensic Genetics Unit, Palermo, Italy
| | - G Matullo
- Department of Medical Sciences, University of Turin, Italy; HuGeF, Human Genetics Foundation, Turin, Italy
| | - A L Nutini
- SOD Genetics Diagnostics, Forensic Genetics, Azienda Ospedaliera Universitaria Careggi, Florence, Italy
| | - V Onofri
- Section of Legal Medicine, Università Politecnica Delle Marche, Ancona, Italy
| | - A Piccinini
- Dipartimento di Scienze Biomediche per la Salute, Università degli Studi di Milano, Italy
| | - M Piglionica
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - E Ponzano
- Department of Molecular Medicine, University of Padova, Italy
| | - C Previderè
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Italy
| | - N Resta
- Department of Biomedical Sciences and Human Oncology, Medical Genetics Unit, "Aldo Moro" University of Bari, Italy
| | - F Scarnicci
- Istituto di Medicina Legale, Università Cattolica del Sacro Cuore, Roma, Italy
| | - G Seidita
- Department of Biopathology, Medical and Forensic Biotechnologies, University of Palermo, Italy
| | | | - S Turrina
- Dipartimento di Sanità Pubblica e Medicina di Comunità, Università degli Studi di Verona, Italy
| | - A Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, Italy
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
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Toscanini U, Gusmão L, Álava Narváez MC, Álvarez JC, Baldassarri L, Barbaro A, Berardi G, Betancor Hernández E, Camargo M, Carreras-Carbonell J, Castro J, Costa SC, Coufalova P, Domínguez V, Fagundes de Carvalho E, Ferreira STG, Furfuro S, García O, Goios A, González R, de la Vega AG, Gorostiza A, Hernández A, Jiménez Moreno S, Lareu MV, León Almagro A, Marino M, Martínez G, Miozzo MC, Modesti NM, Onofri V, Pagano S, Pardo Arias B, Pedrosa S, Penacino GA, Pontes ML, Porto MJ, Puente-Prieto J, Pérez RR, Ribeiro T, Rodríguez Cardozo B, Rodríguez Lesmes YM, Sala A, Santiago B, Saragoni VG, Serrano A, Streitenberger ER, Torres Morales MA, Vannelli Rey SA, Velázquez Miranda M, Whittle MR, Fernández K, Salas A. Analysis of uni and bi-parental markers in mixture samples: Lessons from the 22nd GHEP-ISFG Intercomparison Exercise. Forensic Sci Int Genet 2016; 25:63-72. [PMID: 27500650 DOI: 10.1016/j.fsigen.2016.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 04/21/2016] [Revised: 07/14/2016] [Accepted: 07/17/2016] [Indexed: 10/21/2022]
Abstract
Since 1992, the Spanish and Portuguese-Speaking Working Group of the ISFG (GHEP-ISFG) has been organizing annual Intercomparison Exercises (IEs) coordinated by the Quality Service at the National Institute of Toxicology and Forensic Sciences (INTCF) from Madrid, aiming to provide proficiency tests for forensic DNA laboratories. Each annual exercise comprises a Basic (recently accredited under ISO/IEC 17043: 2010) and an Advanced Level, both including a kinship and a forensic module. Here, we show the results for both autosomal and sex-chromosomal STRs, and for mitochondrial DNA (mtDNA) in two samples included in the forensic modules, namely a mixture 2:1 (v/v) saliva/blood (M4) and a mixture 4:1 (v/v) saliva/semen (M8) out of the five items provided in the 2014 GHEP-ISFG IE. Discrepancies, other than typos or nomenclature errors (over the total allele calls), represented 6.5% (M4) and 4.7% (M8) for autosomal STRs, 15.4% (M4) and 7.8% (M8) for X-STRs, and 1.2% (M4) and 0.0% (M8) for Y-STRs. Drop-out and drop-in alleles were the main cause of errors, with laboratories using different criteria regarding inclusion of minor peaks and stutter bands. Commonly used commercial kits yielded different results for a micro-variant detected at locus D12S391. In addition, the analysis of electropherograms revealed that the proportions of the contributors detected in the mixtures varied among the participants. In regards to mtDNA analysis, besides important discrepancies in reporting heteroplasmies, there was no agreement for the results of sample M4. Thus, while some laboratories documented a single control region haplotype, a few reported unexpected profiles (suggesting contamination problems). For M8, most laboratories detected only the haplotype corresponding to the saliva. Although the GHEP-ISFG has already a large experience in IEs, the present multi-centric study revealed challenges that still exist related to DNA mixtures interpretation. Overall, the results emphasize the need for further research and training actions in order to improve the analysis of mixtures among the forensic practitioners.
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Affiliation(s)
- U Toscanini
- PRICAI-Fundación Favaloro, Buenos Aires, Argentina.
| | - L Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil; IPATIMUP (Institute of Pathology and Molecular Immunology from de University of Porto), Porto, Portugal; I3s (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), Porto, Portugal
| | - M C Álava Narváez
- Laboratorio de Genética Regional Bogotá del Instituto Nacional de Medicina Legal y Ciencias Forenses., Bogotá, Colombia
| | - J C Álvarez
- Lab. de Identificación Genética. Depto. de Medicina Legal, Toxicología y Antropología Física. Facultad de Medicina. Universidad de Granada, Granada, Spain
| | - L Baldassarri
- Institute of Public Sanity Section of Legal Medicine Catholic University of Sacred Heart, Rome, Rome, Italy
| | - A Barbaro
- Studio Indagini Mediche E Forensi (SIMEF), Reggio Calabria, Italy
| | - G Berardi
- PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | - E Betancor Hernández
- Laboratorio Genética Forense, Instituto de Medicina Legal de Las Palmas, ULPG., Las Palmas, Spain
| | - M Camargo
- Laboratorio de Genética Regional Suroccidente del Instituto Nacional de Medicina Legal y Ciencias Forenses., Cali, Colombia
| | - J Carreras-Carbonell
- Policia de la Generalitat - Mossos d'Esquadra, Divisió de Policia Científica, Unitat Central del Laboratori Biològic, Sabadell, Barcelona, Spain
| | - J Castro
- Genética Forense, Unidad Criminalistica Contra la Vulneración de Derechos Fundamentales, Ministerio Público, Venezuela
| | - S C Costa
- Laboratório de Polícia Científica da Polícia Judiciária, Lisbon, Portugal
| | - P Coufalova
- Institute of Criminalistics Prague, Prague, Czech Republic
| | - V Domínguez
- Lab. Biológico de la Dirección Nacional de Policía Científica, Montevideo, Uruguay
| | - E Fagundes de Carvalho
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - S T G Ferreira
- Instituto de Pesquisa de DNA Forense, IPDNA, Polícia Civil do Distrito Federal, PCDF, Brasília, Brazil, and Secretaria Nacional de Segurança Pública do Ministério da Justiça, SENASP/MJ, Brasília, Brazil
| | - S Furfuro
- Laboratorio de Análisis de ADN- Facultad de Ciencias Médicas- Universidad Nacional de Cuyo, Mendoza, Argentina
| | - O García
- Forensic Science Unit, Forensic Genetics Section, Basque Country Police-Ertzaintza, Erandio, Bizkaia, Spain
| | - A Goios
- IPATIMUP (Institute of Pathology and Molecular Immunology from de University of Porto), Porto, Portugal; I3s (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), Porto, Portugal
| | - R González
- Registro Nacional de ADN, Chile, Santiago de Chile, Chile
| | | | | | - A Hernández
- Instituto Nacional de Toxicología y Ciencias Forenses, Delegación en Canarias, Santa Cruz de Tenerife, Spain
| | - S Jiménez Moreno
- Laboratorio de Biología Forense. Dpto Patología y Cirugía. Universidad Miguel Hernández, Elche, Alicante, Spain
| | - M V Lareu
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - A León Almagro
- Comisaría General de Policía Científica - Laboratorio de ADN, Madrid, Spain
| | - M Marino
- Laboratorio de Genética Forense, Poder Judicial de Mendoza, Mendoza, Argentina
| | - G Martínez
- Servicio de Genética Forense, Superior Tribunal de Justicia de Entre Ríos, Paraná, Argentina
| | - M C Miozzo
- Laboratorio Regional de Genética Forense del NOA - Departamento Médico - Poder Judicial de Jujuy, Jujuy, Argentina
| | - N M Modesti
- Instituto de Genética Forense. Poder Judicial de Córdoba, Córdoba, Argentina
| | - V Onofri
- Universita' Politecnica Delle Marche, DSBSP, Section of Legal Medicine, Ancona, Italy
| | | | - B Pardo Arias
- Instituto Nacional de Toxicología y Ciencias Forenses, Departamento de Sevilla, Sevilla, Spain
| | | | - G A Penacino
- Unidad de Analisis de ADN, Colegio Oficial de Farmaceuticos y Bioquímicos, Buenos Aires, Argentina
| | - M L Pontes
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P. - Delegação do Norte, Porto, Portugal
| | - M J Porto
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P., Coimbra, Portugal
| | - J Puente-Prieto
- LabGenetics. Laboratorio de Genética Clínica S.L., Madrid, Spain
| | | | - T Ribeiro
- Serviço de Genética e Biologia Forenses, Instituto Nacional de Medicina Legal e Ciências Forenses, I.P.-Delegação Sul, Lisbon, Portugal
| | | | - Y M Rodríguez Lesmes
- Laboratorio de Biología y Genética Regional Noroccidente del Instituto Nacional de Medicina Legal y Ciencias Forenses., Medellín, Colombia
| | - A Sala
- Servicio de Huellas Digitales Genéticas-Fac. Farmacia y Bioquímica-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - B Santiago
- Instituto Nacional de Toxicología y Ciencias Forenses, Departamento de Madrid. Servicio de Biología., Madrid, Spain
| | - V G Saragoni
- Unidad de Genética Forense, Servicio Médico Legal, Santiago, Chile
| | - A Serrano
- Instituto Nacional de Toxicología y Ciencias Forenses, Departamento de Barcelona, Barcelona, Spain
| | | | | | - S A Vannelli Rey
- Laboratorio Regional Patagonia Norte de Genética Forense - Poder Judicial de Río Negro, Bariloche, Argentina
| | | | - M R Whittle
- Genomic Engenharia Molecular, Sao Paulo, Brazil
| | - K Fernández
- Instituto Nacional de Toxicología y Ciencias Forenses, Departamento de Madrid. Servicio de Biología., Madrid, Spain
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPop Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
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7
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Purps J, Siegert S, Willuweit S, Nagy M, Alves C, Salazar R, Angustia SMT, Santos LH, Anslinger K, Bayer B, Ayub Q, Wei W, Xue Y, Tyler-Smith C, Bafalluy MB, Martínez-Jarreta B, Egyed B, Balitzki B, Tschumi S, Ballard D, Court DS, Barrantes X, Bäßler G, Wiest T, Berger B, Niederstätter H, Parson W, Davis C, Budowle B, Burri H, Borer U, Koller C, Carvalho EF, Domingues PM, Chamoun WT, Coble MD, Hill CR, Corach D, Caputo M, D'Amato ME, Davison S, Decorte R, Larmuseau MHD, Ottoni C, Rickards O, Lu D, Jiang C, Dobosz T, Jonkisz A, Frank WE, Furac I, Gehrig C, Castella V, Grskovic B, Haas C, Wobst J, Hadzic G, Drobnic K, Honda K, Hou Y, Zhou D, Li Y, Hu S, Chen S, Immel UD, Lessig R, Jakovski Z, Ilievska T, Klann AE, García CC, de Knijff P, Kraaijenbrink T, Kondili A, Miniati P, Vouropoulou M, Kovacevic L, Marjanovic D, Lindner I, Mansour I, Al-Azem M, Andari AE, Marino M, Furfuro S, Locarno L, Martín P, Luque GM, Alonso A, Miranda LS, Moreira H, Mizuno N, Iwashima Y, Neto RSM, Nogueira TLS, Silva R, Nastainczyk-Wulf M, Edelmann J, Kohl M, Nie S, Wang X, Cheng B, Núñez C, Pancorbo MMD, Olofsson JK, Morling N, Onofri V, Tagliabracci A, Pamjav H, Volgyi A, Barany G, Pawlowski R, Maciejewska A, Pelotti S, Pepinski W, Abreu-Glowacka M, Phillips C, Cárdenas J, Rey-Gonzalez D, Salas A, Brisighelli F, Capelli C, Toscanini U, Piccinini A, Piglionica M, Baldassarra SL, Ploski R, Konarzewska M, Jastrzebska E, Robino C, Sajantila A, Palo JU, Guevara E, Salvador J, Ungria MCD, Rodriguez JJR, Schmidt U, Schlauderer N, Saukko P, Schneider PM, Sirker M, Shin KJ, Oh YN, Skitsa I, Ampati A, Smith TG, Calvit LSD, Stenzl V, Capal T, Tillmar A, Nilsson H, Turrina S, De Leo D, Verzeletti A, Cortellini V, Wetton JH, Gwynne GM, Jobling MA, Whittle MR, Sumita DR, Wolańska-Nowak P, Yong RYY, Krawczak M, Nothnagel M, Roewer L. A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Sci Int Genet 2014; 12:12-23. [PMID: 24854874 PMCID: PMC4127773 DOI: 10.1016/j.fsigen.2014.04.008] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/19/2014] [Indexed: 02/05/2023]
Abstract
In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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Affiliation(s)
- Josephine Purps
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Sabine Siegert
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Sascha Willuweit
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Marion Nagy
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
| | - Cíntia Alves
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Renato Salazar
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | | | - Lorna H Santos
- Philippine National Police Crime Laboratory, Quezon City, Philippines
| | - Katja Anslinger
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Birgit Bayer
- Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Wei Wei
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | | | - Balazs Egyed
- GenoID Forensic DNA Laboratory, Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Beate Balitzki
- Institut für Rechtsmedizin, Universität Basel, Switzerland
| | | | - David Ballard
- Department of Forensic and Analytical Science, King's College London, London, UK
| | | | - Xinia Barrantes
- Forensic Sciences Department, Poder Judicial, Heredia, Costa Rica
| | | | - Tina Wiest
- Landeskriminalamt Baden-Württemberg, Germany
| | - Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
| | | | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA
| | - Carey Davis
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA
| | - Bruce Budowle
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Helen Burri
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | - Urs Borer
- Forensische Genetik, Kantonsspital Aarau AG, Switzerland
| | | | - Elizeu F Carvalho
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | - Patricia M Domingues
- Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
| | | | - Michael D Coble
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Carolyn R Hill
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Daniel Corach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Mariela Caputo
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
| | - Maria E D'Amato
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Sean Davison
- University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
| | - Ronny Decorte
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Maarten H D Larmuseau
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Claudio Ottoni
- KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
| | - Olga Rickards
- Centre of Molecular Antropology For Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Italy
| | - Di Lu
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Chengtao Jiang
- Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Tadeusz Dobosz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - Anna Jonkisz
- Institute of Forensic Medicine, Medical University, Wroclaw, Poland
| | - William E Frank
- Illinois State Police, Research & Development Laboratory, Springfield, USA
| | - Ivana Furac
- Department of Forensic Medicine and Criminology, University of Zagreb, Croatia
| | - Christian Gehrig
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Vincent Castella
- University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
| | - Branka Grskovic
- Forensic Science Centre "Ivan Vucetic", General Police Directorate, Ministry of Interior, Zagreb, Croatia
| | - Cordula Haas
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | - Jana Wobst
- Institut für Rechtsmedizin, Universität Zürich, Switzerland
| | | | | | - Katsuya Honda
- Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, Japan
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Di Zhou
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Yan Li
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
| | - Shengping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | - Shenglan Chen
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
| | | | | | - Zlatko Jakovski
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Tanja Ilievska
- Institute for Forensic Medicine and Criminalistics, Medical Faculty, University "Ss. Cyril and Methodius", Skopje, Macedonia
| | - Anja E Klann
- Institut für Rechtsmedizin, Universitätsmedizin Greifswald, Germany
| | | | - Peter de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thirsa Kraaijenbrink
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aikaterini Kondili
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Penelope Miniati
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Maria Vouropoulou
- Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. - Hellenic Police, Athens, Greece
| | - Lejla Kovacevic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanovic
- Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Iris Lindner
- Institut für Rechtsmedizin, Universität Rostock, Germany
| | - Issam Mansour
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Mouayyad Al-Azem
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Ansar El Andari
- Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
| | - Miguel Marino
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Sandra Furfuro
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Laura Locarno
- Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
| | - Pablo Martín
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Gracia M Luque
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | - Antonio Alonso
- Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
| | | | - Helena Moreira
- Departamento de Biologia, Universidade de Aveiro, Portugal
| | - Natsuko Mizuno
- National Research Institute of Police Science, Chiba, Japan
| | | | - Rodrigo S Moura Neto
- Instituto de Biologia, Universidade Federal do Rio de Janeiro and DIMAV/INMETRO, Brazil
| | | | - Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | | | | | - Michael Kohl
- Institut für Rechtsmedizin, Universität Leipzig, Germany
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xianping Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | - Baowen Cheng
- Department of Criminal Investigation, Yunnan Provincial Public Security Bureau, Kunming, China
| | - Carolina Núñez
- BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain
| | | | - Jill K Olofsson
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Valerio Onofri
- Section of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
| | | | - Horolma Pamjav
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Antonia Volgyi
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Gusztav Barany
- DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
| | - Ryszard Pawlowski
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Agnieszka Maciejewska
- Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
| | - Susi Pelotti
- Department of Medical and Surgical Sciences (DIMEC), Institute of Legal Medicine, School of Medicine, University of Bologna, Italy
| | - Witold Pepinski
- Department of Forensic Medicine, Medical University of Bialystok, Poland
| | | | - Christopher Phillips
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Jorge Cárdenas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Danel Rey-Gonzalez
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
| | - Francesca Brisighelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; Department of Zoology, University of Oxford, Oxford, UK
| | - Ulises Toscanini
- Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain; PRICAI-Fundación Favaloro, Buenos Aires, Argentina
| | - Andrea Piccinini
- Forensic Genetics Laboratory, Department of Human Morphology and Biomedical Sciences, Università degli Studi di Milano, Italy
| | - Marilidia Piglionica
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Stefania L Baldassarra
- Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
| | - Rafal Ploski
- Department of Medical Genetics, Warsaw Medical University, Poland
| | | | | | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Antti Sajantila
- Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA; Department of Forensic Medicine, University of Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Evelyn Guevara
- Department of Forensic Medicine, University of Helsinki, Finland
| | - Jazelyn Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Maria Corazon De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
| | - Jae Joseph Russell Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines; Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
| | - Ulrike Schmidt
- Institut für Rechtsmedizin, Universitätsklinikum Freiburg, Germany
| | | | - Pekka Saukko
- Department of Forensic Medicine, University of Turku, Finland
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Miriam Sirker
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Yu Na Oh
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Iulia Skitsa
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Alexandra Ampati
- Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
| | - Tobi-Gail Smith
- Department of Basic Medical Sciences, University of the West Indies, Kingston, Jamaica
| | | | - Vlastimil Stenzl
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Thomas Capal
- Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Helena Nilsson
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Stefania Turrina
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Domenico De Leo
- Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
| | - Andrea Verzeletti
- Istituto di Medicina Legale, Universitá degli Studi di Brescia, Italy
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, UK
| | | | | | | | | | | | - Rita Y Y Yong
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.
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Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q, Balažic J, Ballantyne J, Ballard DJ, Berger B, Bobillo C, Bouabdellah M, Burri H, Capal T, Caratti S, Cárdenas J, Cartault F, Carvalho EF, Carvalho M, Cheng B, Coble MD, Comas D, Corach D, D'Amato ME, Davison S, de Knijff P, De Ungria MCA, Decorte R, Dobosz T, Dupuy BM, Elmrghni S, Gliwiński M, Gomes SC, Grol L, Haas C, Hanson E, Henke J, Henke L, Herrera-Rodríguez F, Hill CR, Holmlund G, Honda K, Immel UD, Inokuchi S, Jobling MA, Kaddura M, Kim JS, Kim SH, Kim W, King TE, Klausriegler E, Kling D, Kovačević L, Kovatsi L, Krajewski P, Kravchenko S, Larmuseau MHD, Lee EY, Lessig R, Livshits LA, Marjanović D, Minarik M, Mizuno N, Moreira H, Morling N, Mukherjee M, Munier P, Nagaraju J, Neuhuber F, Nie S, Nilasitsataporn P, Nishi T, Oh HH, Olofsson J, Onofri V, Palo JU, Pamjav H, Parson W, Petlach M, Phillips C, Ploski R, Prasad SPR, Primorac D, Purnomo GA, Purps J, Rangel-Villalobos H, Rębała K, Rerkamnuaychoke B, Gonzalez DR, Robino C, Roewer L, Rosa A, Sajantila A, Sala A, Salvador JM, Sanz P, Schmitt C, Sharma AK, Silva DA, Shin KJ, Sijen T, Sirker M, Siváková D, Skaro V, Solano-Matamoros C, Souto L, Stenzl V, Sudoyo H, Syndercombe-Court D, Tagliabracci A, Taylor D, Tillmar A, Tsybovsky IS, Tyler-Smith C, van der Gaag KJ, Vanek D, Völgyi A, Ward D, Willemse P, Yap EPH, Yong RYY, Pajnič IZ, Kayser M. Toward male individualization with rapidly mutating y-chromosomal short tandem repeats. Hum Mutat 2014; 35:1021-32. [PMID: 24917567 PMCID: PMC4145662 DOI: 10.1002/humu.22599] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/26/2014] [Indexed: 11/30/2022]
Abstract
Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.
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Affiliation(s)
- Kaye N Ballantyne
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, Victoria, Australia
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Sartori N, Onofri V, Parpinelli V, Almeida C, Gimenes V, Neves Barbosa R, Martins J. 1518 – Demographic and epidemiological profile of outpatients with mental disorders on depot medication in a mental health teaching hospital clinic of marilia/sp/brazil. Eur Psychiatry 2013. [DOI: 10.1016/s0924-9338(13)76535-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Tagliabracci A, Onofri V, Previderè C, Schneider PM, De Stefano F. The Ge.F.I. DNA Proficiency Test: Year-one experience. Forensic Science International: Genetics Supplement Series 2013. [DOI: 10.1016/j.fsigss.2013.10.013] [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: 12/01/2022]
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Presciuttini S, Toni C, Alù M, Asmundo A, Baldassarri L, Barbaro A, Caenazzo L, Carnevali E, Cerri N, D’Aloia E, Di Nunzio C, Onofri V, Peloso G, Pelotti S, Piccinini A, Robino C, Turrina S, Venturi M, Domenici R. X-chromosome in Italy: A database of 29 STR markers. Forensic Science International: Genetics Supplement Series 2011. [DOI: 10.1016/j.fsigss.2011.08.018] [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: 11/26/2022]
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Kožul V, Glavić N, Tutman P, Bolotin J, Onofri V. The spawning, embryonic and early larval development of the green wrasse Labrus viridis (Linnaeus, 1758) (Labridae) in controlled conditions. Anim Reprod Sci 2011; 125:196-203. [PMID: 21342751 DOI: 10.1016/j.anireprosci.2011.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 01/17/2011] [Accepted: 01/24/2011] [Indexed: 11/26/2022]
Abstract
Green wrasse, Labrus viridis (Linnaeus, 1758), is an endangered species in the southern Adriatic Sea, but it is also of interest for potential rearing in polyculture with other commercial species for the repopulation of areas where it is endangered or as a new aquaculture species. A parental stock of the green wrasse was kept in aquaria for six years. The spawning, embryonic and early larval development maintained under controlled laboratory conditions are described and illustrated. The average diameter of newly spawned eggs was 1.01±0.03 mm. Mature and fertilized eggs were attached to the tank bottom by mucus. Hatching started after 127 h at a mean temperature of 14.4±0.8°C. The average total length of newly hatched larvae was 4.80±0.22 mm. Absorption of the yolk-sac was completed after the 5th day when larvae reached 5.87±0.28 mm. Larvae were fed with the rotifers Brachionus plicatilis. The pigmentation of L. viridis larvae is similar to that of Labrus merula and Labrus bergylta, but the main differences between these species are in the size of larvae and the development time of the melanophores on the anal fin-fold (five days later than with L. merula) and on top of the head (nine days earlier than with L. merula).
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Affiliation(s)
- V Kožul
- Institute for Marine and Coastal Research, 20000 Dubrovnik, Croatia.
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Onofri V, Buscemi L, Tagliabracci A. Evaluating Y-chromosome STRs mutation rates: A collaborative study of the Ge.F.I.-ISFG Italian Group. Forensic Science International: Genetics Supplement Series 2009. [DOI: 10.1016/j.fsigss.2009.08.167] [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: 10/20/2022]
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Turchi C, Buscemi L, Giacchino E, Onofri V, Fendt L, Parson W, Tagliabracci A. Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: An enrichment of forensic mtDNA databases with Northern Africa data. Forensic Sci Int Genet 2009; 3:166-72. [DOI: 10.1016/j.fsigen.2009.01.014] [Citation(s) in RCA: 25] [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: 11/16/2022]
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Tofanelli S, Ferri G, Bulayeva K, Caciagli L, Onofri V, Taglioli L, Bulayev O, Boschi I, Alù M, Berti A, Rapone C, Beduschi G, Luiselli D, Cadenas AM, Awadelkarim KD, Mariani-Costantini R, Elwali NE, Verginelli F, Pilli E, Herrera RJ, Gusmão L, Paoli G, Capelli C. J1-M267 Y lineage marks climate-driven pre-historical human displacements. Eur J Hum Genet 2009; 17:1520-4. [PMID: 19367321 DOI: 10.1038/ejhg.2009.58] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The present day distribution of Y chromosomes bearing the haplogroup J1 M267(*)G variant has been associated with different episodes of human demographic history, the main one being the diffusion of Islam since the Early Middle Ages. To better understand the modes and timing of J1 dispersals, we reconstructed the genealogical relationships among 282 M267(*)G chromosomes from 29 populations typed at 20 YSTRs and 6 SNPs. Phylogenetic analyses depicted a new genetic background consistent with climate-driven demographic dynamics occurring during two key phases of human pre-history: (1) the spatial expansion of hunter gatherers in response to the end of the late Pleistocene cooling phases and (2) the displacement of groups of foragers/herders following the mid-Holocene rainfall retreats across the Sahara and Arabia. Furthermore, J1 STR motifs previously used to trace Arab or Jewish ancestries were shown unsuitable as diagnostic markers for ethnicity.
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Turchi C, Buscemi L, Piva F, Alessandrini F, Onofri V, Principato G, Tagliabracci A. Association of genetic variations in alcohol dehydrogenase 4 with alcohol dependence in Italian population sample. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.127] [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: 11/28/2022]
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Onofri V, Giacomini I, Alessandrini F, Turchi C, Buscemi L, Tagliabracci A. Population data for D10S1248, D14S1434, and D22S1045 miniSTRs loci from the Marches region (Central Italy). Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.038] [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: 10/22/2022]
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Onofri V, Alessandrini F, Turchi C, Pesaresi M, Tagliabracci A. Y-chromosome markers distribution in Northern Africa: High-resolution SNP and STR analysis in Tunisia and Morocco populations. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.173] [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: 10/22/2022]
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Ferri G, Robino C, Alù M, Luiselli D, Tofanelli S, Caciagli L, Onofri V, Pelotti S, Di Gaetano C, Crobu F, Beduschi G, Capelli C. Molecular characterisation and population genetics of the DYS458 .2 allelic variant. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.217] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [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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Onofri V, Tagliabracci A, Boschi I, Brisighelli F, Scarnicci F, Pascali VL, Ferri G, Pelotti S, Capelli C. Y chromosome J2 subtyping in an Italian sample: Population and forensic implications. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.170] [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: 11/28/2022]
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Onofri V, Alessandrini F, Turchi C, Fraternale B, Buscemi L, Pesaresi M, Tagliabracci A. Y-chromosome genetic structure in sub-Apennine populations of Central Italy by SNP and STR analysis. Int J Legal Med 2007; 121:234-7. [PMID: 17287987 DOI: 10.1007/s00414-007-0153-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [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: 08/18/2006] [Accepted: 12/22/2006] [Indexed: 11/27/2022]
Abstract
To define the Y-chromosome genetic structure in Apennine populations, 17 Y-chromosome short tandem repeats (Y-STRs) and 37 Y-single nucleotide polymorphisms (Y-SNPs) were typed in 162 subjects living in the upland area of the Marches (Central Italy). A total number of 155 haplotypes (haplotype diversity was 0.9994) and 14 SNP haplogroups were observed. Testing high-resolution Y-chromosome data sets, e.g. using Yfiler and SNPs, increases the discriminatory capacity in individual identification for forensic purposes. It is also useful in autochthonous population and micro-population studies to highlight the most informative loci for evolutionary aims.
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Affiliation(s)
- Valerio Onofri
- Institute of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
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Onofri V, Alessandrini F, Turchi C, Pesaresi M, Buscemi L, Tagliabracci A. Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs. Forensic Sci Int 2006; 157:23-35. [PMID: 15896936 DOI: 10.1016/j.forsciint.2005.03.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [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: 11/30/2004] [Revised: 03/08/2005] [Accepted: 03/22/2005] [Indexed: 11/23/2022]
Abstract
This work describes an efficient and rapid test for typing 37 single nucleotide polymorphisms (SNPs) of the non-recombining region of Y chromosome (NRY) from a minimal amount of DNA using six PCR multiplexes. Markers were drawn following a hierarchical strategy based on the phylogenetic tree of Y chromosome proposed by the Y Chromosome Consortium [The Y Chromosome Consortium, A nomenclature system for the tree of human Y-chromosomal binary haplogroups, Genome Res. 12 (2002) 339-348]. Two multiplexes--arbitrarily named MY1 and MY2--were developed to explore the basal branches of the tree encompassing all the major clades A-R: MY1 for markers M35, M89, M172, M170, M9, M173, M45 and MY2 for markers M52, M216, M174, M181, M201, M91, M96, M214. Four multiplexes able of typing the more superficial branches typical of most frequent European haplogroups E3b, J2, R1 and I, were also developed and named MY-E3b (M78, M107, M224, M165, M148, M81), MY-J2 (M158, M68, M47, M102, M137, M67), MY-R1 (M17, M269, M18, P25, SRY10831.2) and MY-I (M72, M223, M26, M21, M161). SNP genotyping was carried out by hot-start PCR amplification with primers yielding fragments between 63 and 210 nucleotides, followed by minisequencing reaction based on dideoxy single-base extension and capillary electrophoresis of extension products. The sequential application of these multiplexes is a robust and effective resource for typing the most frequent European Y-SNP haplogroups, and appears to be suitable for forensic purposes and evolutionary studies.
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Affiliation(s)
- Valerio Onofri
- Istituto di Medicina Legale, Università Politecnica delle Marche, Policlinico Torrette, Ancona, Italy
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Alessandrini F, Turchi C, Onofri V, Buscemi L, Pesaresi M, Tagliabracci A. Multiplex PCR development of Y-chromosomal biallelic polymorphisms for forensic application. J Forensic Sci 2005; 50:519-25. [PMID: 15932081] [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: 05/02/2023]
Abstract
Single-nucleotide polymorphisms of Y chromosome (Y-SNPs) are a class of markers of interest in forensic investigations, because many of them show regional specificity, providing useful information about the geographic origin of a subject or evidence under investigation. A first multiplex with 7 SNPs (M35, M89, M9, M170, M172, M45, M173), which occur in the basal branches of the phylogenetic tree and are able to assign a subject to known most frequent European haplogroups, was designed. SNP genotyping was accomplished by hot-start PCR with primers amplifying fragments between 96 and 136 nucleotides, minisequencing, and capillary electrophoresis of extension products. Ninety seven subjects of known geographic provenance were studied, of which 68 from Europe. Of these, 57 had mutations found more frequently in European haplogroups and 11 more frequent in Asian populations. Subjects from non-European countries were also examined and had haplogroups common in their regions of provenance. Experiments with low molecular weight DNA gave positive amplification from 1 ng of DNA for all seven SNPs.
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Affiliation(s)
- Federica Alessandrini
- Istituto di Medicina Legale, Università Politecnica delle Marche, I-60020 Ancona, Italy
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Turchi C, Pesaresi M, Alessandrini F, Onofri V, Arseni A, Tagliabracci A. Unusual association of three rare alleles and a mismatch in a case of paternity testing. J Forensic Sci 2004; 49:260-2. [PMID: 15027541] [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: 04/29/2023]
Abstract
This study reports a paternity case analyzed by the AmpFlSTR Identifiler Kit (AB) in which father and daughter shared three rare alleles for D19S433, D18S51 and TH01 microsatellites. The case also showed an apparent exclusion, due to a mutation at the D3S 1358 microsatellite. Sequencing analysis was performed to assess the size of the rare alleles and to establish their structure, which revealed some molecular variations in regions flanking the motif repeats.
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Affiliation(s)
- Chiara Turchi
- Istituto di Medicina Legale, Universita di Ancona, Policlinico Torrette, 1-60020 Ancona, Italy
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