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Tao R, Wang S, Zhang J, Zhang J, Yang Z, Sheng X, Hou Y, Zhang S, Li C. Separation/extraction, detection, and interpretation of DNA mixtures in forensic science (review). Int J Legal Med 2018; 132:1247-1261. [PMID: 29802461 DOI: 10.1007/s00414-018-1862-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/11/2018] [Indexed: 02/08/2023]
Abstract
Interpreting mixed DNA samples containing material from multiple contributors has long been considered a major challenge in forensic casework, especially when encountering low-template DNA (LT-DNA) or high-order mixtures that may involve missing alleles (dropout) and unrelated alleles (drop-in), among others. In the last decades, extraordinary progress has been made in the analysis of mixed DNA samples, which has led to increasing attention to this research field. The advent of new methods for the separation and extraction of DNA from mixtures, novel or jointly applied genetic markers for detection and reliable interpretation approaches for estimating the weight of evidence, as well as the powerful massively parallel sequencing (MPS) technology, has greatly extended the range of mixed samples that can be correctly analyzed. Here, we summarized the investigative approaches and progress in the field of forensic DNA mixture analysis, hoping to provide some assistance to forensic practitioners and to promote further development involving this issue.
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Affiliation(s)
- Ruiyang Tao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jiashuo Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Jingyi Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Zihao Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Medicine, School of Basic Medical Science, Wenzhou Medical University, Wenzhou, 325035, People's Republic of China
| | - Xiang Sheng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.,Department of Forensic Science, Medical School of Soochow University, Suzhou, 215123, People's Republic of China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Suhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
| | - Chengtao Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, People's Republic of China. .,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Sciences, Shanghai, 200063, People's Republic of China.
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Towards more efficient large-scale DNA-based detection of terrestrial mammal predators from scats. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0369-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Heinz T, Pala M, Gómez-Carballa A, Richards MB, Salas A. Updating the African human mitochondrial DNA tree: Relevance to forensic and population genetics. Forensic Sci Int Genet 2016; 27:156-159. [PMID: 28086175 DOI: 10.1016/j.fsigen.2016.12.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 12/14/2016] [Accepted: 12/30/2016] [Indexed: 11/24/2022]
Abstract
Analysis of human mitochondrial DNA (mtDNA) variation plays an important role in forensic genetic investigations, especially in degraded biological samples and hair shafts. There are many issues of the mtDNA phylogeny that are of special interest to the forensic community, such as haplogroup classification or the post hoc investigation of potential errors in mtDNA datasets. We have analyzed >2200 mitogenomes of African ancestry with the aim of improving the known worldwide phylogeny. More than 300 new minor subclades were identified, and the Time to the Most Recent Common Ancestor (TMRCA) was estimated for each node of the phylogeny. Phylogeographic details are provided which might also be relevant to forensic genetics. The present study has special interest for forensic investigations because current analysis and interpretation of mtDNA casework rest on a solid worldwide phylogeny, as is evident from the role that phylogeny plays in popular resources in the field (e.g. PhyloTree), software (e.g. Haplogrep 2), and databases (e.g. EMPOP). Apart from this forensic genetic interest, we also highlight the impact of this research in anthropological studies, such as those related to the reconstruction of the transatlantic slave trade.
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Affiliation(s)
- Tanja Heinz
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
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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: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [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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Ramsey DSL, MacDonald AJ, Quasim S, Barclay C, Sarre SD. An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania. J Appl Ecol 2015. [DOI: 10.1111/1365-2664.12407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David S. L. Ramsey
- Department of Environment, Land Water and Planning; Arthur Rylah Institute; 123 Brown Street Heidelberg Vic. 3084 Australia
- School of Earth and Environmental Sciences; University of Adelaide; Adelaide SA 5005 Australia
| | - Anna J. MacDonald
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2616 Australia
| | - Sumaiya Quasim
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2616 Australia
| | - Candida Barclay
- Department of Primary Industry, Parks, Water and the Environment; 171 Westbury Road Prospect TAS 7250 Australia
| | - Stephen D. Sarre
- Institute for Applied Ecology; University of Canberra; Canberra ACT 2616 Australia
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Söchtig J, Álvarez-Iglesias V, Mosquera-Miguel A, Gelabert-Besada M, Gómez-Carballa A, Salas A. Genomic insights on the ethno-history of the Maya and the 'Ladinos' from Guatemala. BMC Genomics 2015; 16:131. [PMID: 25887241 PMCID: PMC4422311 DOI: 10.1186/s12864-015-1339-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background Guatemala is a multiethnic and multilingual country located in Central America. The main population groups separate ‘Ladinos’ (mixed Native American-African-Spanish), and Native indigenous people of Maya descent. Among the present-day Guatemalan Maya, there are more than 20 different ethnic groups separated by different languages and cultures. Genetic variation of these communities still remains largely unexplored. The principal aim of this study is to explore the genetic variability of the Maya and ‘Ladinos’ from Guatemala by means of uniparental and ancestry informative markers (AIMs). Results Analyses of uniparental genetic markers indicate that Maya have a dominant Native American ancestry (mitochondrial DNA [mtDNA]: 100%; Y-chromosome: 94%). ‘Ladino’, however, show a clear gender-bias as indicated by the large European ancestry observed in the Y-chromosome (75%) compared to the mtDNA (0%). Autosomal polymorphisms (AIMs) also mirror this marked gender-bias: (i) Native American ancestry: 92% for the Maya vs. 55% for the ‘Ladino’, and (ii) European ancestry: 8% for the Maya vs. 41% for the ‘Ladino’. In addition, the impact of the Trans-Atlantic slave trade on the present-day Guatemalan population is very low (and only occurs in the ‘Ladino’; mtDNA: 9%; AIMs: 4%), in part mirroring the fact that Guatemala has a predominant orientation to the Pacific Ocean instead of a Caribbean one. Sequencing of entire Guatemalan mitogenomes has led to improved Native American phylogeny via the addition of new haplogroups that are mainly observed in Mesoamerica and/or the North of South America. Conclusions The data reveal the existence of a fluid gene flow in the Mesoamerican area and a predominant unidirectional flow towards South America, most likely occurring during the Pre-Classic (1800 BC-200 AD) and the Classic (200–1000 AD) Eras of the Mesoamerican chronology, coinciding with development of the most distinctive and advanced Mesoamerican civilization, the Maya. Phylogenetic features of mtDNA data also suggest a demographic scenario that is compatible with moderate local endogamy and isolation in the Maya combined with episodes of gene exchange between ethnic groups, suggesting an ethno-genesis in the Guatemalan Maya that is recent and supported on a cultural rather than a biological basis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1339-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jens Söchtig
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Ana Mosquera-Miguel
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Miguel Gelabert-Besada
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, CP 15872, Galicia, Spain.
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DNA Commission of the International Society for Forensic Genetics: Revised and extended guidelines for mitochondrial DNA typing. Forensic Sci Int Genet 2014; 13:134-42. [DOI: 10.1016/j.fsigen.2014.07.010] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 07/19/2014] [Indexed: 11/21/2022]
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Prieto L, Alves C, Zimmermann B, Tagliabracci A, Prieto V, Montesino M, Whittle M, Anjos M, Cardoso S, Heinrichs B, Hernandez A, López-Parra A, Sala A, Saragoni V, Burgos G, Marino M, Paredes M, Mora-Torres C, Angulo R, Chemale G, Vullo C, Sánchez-Simón M, Comas D, Puente J, López-Cubría C, Modesti N, Aler M, Merigioli S, Betancor E, Pedrosa S, Plaza G, Masciovecchio M, Schneider P, Parson W. GHEP-ISFG proficiency test 2011: Paper challenge on evaluation of mitochondrial DNA results. Forensic Sci Int Genet 2013; 7:10-5. [DOI: 10.1016/j.fsigen.2012.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 04/06/2012] [Accepted: 04/20/2012] [Indexed: 11/16/2022]
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Brisighelli F, Álvarez-Iglesias V, Fondevila M, Blanco-Verea A, Carracedo Á, Pascali VL, Capelli C, Salas A. Uniparental markers of contemporary Italian population reveals details on its pre-Roman heritage. PLoS One 2012; 7:e50794. [PMID: 23251386 PMCID: PMC3519480 DOI: 10.1371/journal.pone.0050794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 10/24/2012] [Indexed: 11/18/2022] Open
Abstract
Background According to archaeological records and historical documentation, Italy has been a melting point for populations of different geographical and ethnic matrices. Although Italy has been a favorite subject for numerous population genetic studies, genetic patterns have never been analyzed comprehensively, including uniparental and autosomal markers throughout the country. Methods/Principal Findings A total of 583 individuals were sampled from across the Italian Peninsula, from ten distant (if homogeneous by language) ethnic communities — and from two linguistic isolates (Ladins, Grecani Salentini). All samples were first typed for the mitochondrial DNA (mtDNA) control region and selected coding region SNPs (mtSNPs). This data was pooled for analysis with 3,778 mtDNA control-region profiles collected from the literature. Secondly, a set of Y-chromosome SNPs and STRs were also analyzed in 479 individuals together with a panel of autosomal ancestry informative markers (AIMs) from 441 samples. The resulting genetic record reveals clines of genetic frequencies laid according to the latitude slant along continental Italy – probably generated by demographical events dating back to the Neolithic. The Ladins showed distinctive, if more recent structure. The Neolithic contribution was estimated for the Y-chromosome as 14.5% and for mtDNA as 10.5%. Y-chromosome data showed larger differentiation between North, Center and South than mtDNA. AIMs detected a minor sub-Saharan component; this is however higher than for other European non-Mediterranean populations. The same signal of sub-Saharan heritage was also evident in uniparental markers. Conclusions/Significance Italy shows patterns of molecular variation mirroring other European countries, although some heterogeneity exists based on different analysis and molecular markers. From North to South, Italy shows clinal patterns that were most likely modulated during Neolithic times.
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Affiliation(s)
- Francesca Brisighelli
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Vanesa Álvarez-Iglesias
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Manuel Fondevila
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Alejandro Blanco-Verea
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX-SERGAS), CIBER enfermedades raras, Santiago de Compostela, Galicia, Spain
| | - Vincenzo L. Pascali
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Antonio Salas
- Unidade de Xenética, Facultade de Medicina, Instituto de Medicina Legal, Universidade de Santiago de Compostela, Galicia, Spain
- * E-mail:
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Iglesias P, Salas A, Costoya JA. The maintenance of mitochondrial genetic stability is crucial during the oncogenic process. Commun Integr Biol 2012; 5:34-8. [PMID: 22482007 DOI: 10.4161/cib.18160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The main energetic resources of the cell are the mitochondria. As such, these organelles control a number of processes related to the life and death of the cell and also have a prominent function in the maintenance of tumor cells. In the last years, several authors have proposed an active role for mitochondria in tumorigenesis, more specifically concerning somatic mutations in mitochondrial DNA (mtDNA). Here, we wanted to evaluate this hypothesis based on the conclusions obtained in a model of gliomagenesis with elevated levels of ROS (reactive oxygen species), a toxic by-product of tumor metabolism. According to our findings, none of the mtDNA variants were found relevant to the tumoral process or suggest the involvement of mitochondria in tumorigenesis beyond the metabolic requirements of the tumoral cell. We conclude that there is not enough evidence to support the claim that mitochondrial instability holds any relevant role in the tumoral process.
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A cautionary note on switching mitochondrial DNA reference sequences in forensic genetics. Forensic Sci Int Genet 2012; 6:e182-4. [PMID: 22840856 DOI: 10.1016/j.fsigen.2012.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 06/27/2012] [Accepted: 06/29/2012] [Indexed: 11/24/2022]
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12
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Montesino M, Tagliabracci A, Zimmermann B, Gusmao L, Burgos G, Heinrichs B, Prieto V, Paredes M, Hernandez A, Cardoso S, Vullo C, Marino M, Whittle M, Velázquez M, Sánchez-Simón M, Maxud K, Anjos M, Vargas-Díaz L, López-Parra A, Bobillo C, García-Segura R, Puente J, Pedrosa S, Streintenberger E, Moreno F, Chemale G, Pestano J, Merigioli S, Espinoza M, Comas D, López-Cubría C, Bogus M, Prieto L, Parson W. GHEP-ISFG Proficiency Test 2011: Paper challenge on evaluation of mitochondrial DNA results. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2011. [DOI: 10.1016/j.fsigss.2011.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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A statistical framework for the interpretation of mtDNA mixtures: forensic and medical applications. PLoS One 2011; 6:e26723. [PMID: 22053205 PMCID: PMC3203886 DOI: 10.1371/journal.pone.0026723] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 10/02/2011] [Indexed: 11/19/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) variation is commonly analyzed in a wide range of different biomedical applications. Cases where more than one individual contribute to a stain genotyped from some biological material give rise to a mixture. Most forensic mixture cases are analyzed using autosomal markers. In rape cases, Y-chromosome markers typically add useful information. However, there are important cases where autosomal and Y-chromosome markers fail to provide useful profiles. In some instances, usually involving small amounts or degraded DNA, mtDNA may be the only useful genetic evidence available. Mitochondrial DNA mixtures also arise in studies dealing with the role of mtDNA variation in tumorigenesis. Such mixtures may be generated by the tumor, but they could also originate in vitro due to inadvertent contamination or a sample mix-up. Methods/Principal Findings We present the statistical methods needed for mixture interpretation and emphasize the modifications required for the more well-known methods based on conventional markers to generalize to mtDNA mixtures. Two scenarios are considered. Firstly, only categorical mtDNA data is assumed available, that is, the variants contributing to the mixture. Secondly, quantitative data (peak heights or areas) on the allelic variants are also accessible. In cases where quantitative information is available in addition to allele designation, it is possible to extract more precise information by using regression models. More precisely, using quantitative information may lead to a unique solution in cases where the qualitative approach points to several possibilities. Importantly, these methods also apply to clinical cases where contamination is a potential alternative explanation for the data. Conclusions/Significance We argue that clinical and forensic scientists should give greater consideration to mtDNA for mixture interpretation. The results and examples show that the analysis of mtDNA mixtures contributes substantially to forensic casework and may also clarify erroneous claims made in clinical genetics regarding tumorigenesis.
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Bandelt HJ, Salas A. Current next generation sequencing technology may not meet forensic standards. Forensic Sci Int Genet 2011; 6:143-5. [PMID: 21565569 DOI: 10.1016/j.fsigen.2011.04.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 01/16/2011] [Accepted: 04/02/2011] [Indexed: 11/19/2022]
Abstract
In a Nature paper of 2010, the concern was raised that intra-individual mtDNA variation may be more pronounced than previously believed, in that heteroplasmies are common and vary markedly from tissue to tissue. This claim taken at face value would have considerable impact on forensic casework. It turns out however that the employed technology detected the germ-line variation relative to the reference sequence only incompletely: on average at least five mutations were missed per sample, as an in silico reassessment of the data reveals. Before one can really set out to access to entire mtDNA genome data with relative ease for forensic purposes, one needs careful calibration studies under strict forensic conditions-or might have to wait for another generation.
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15
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Cerezo M, Bandelt HJ, Martín-Guerrero I, Ardanaz M, Vega A, Carracedo Á, García-Orad Á, Salas A. High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia. PLoS One 2009; 4:e7902. [PMID: 19924307 PMCID: PMC2775629 DOI: 10.1371/journal.pone.0007902] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/20/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Chronic Lymphocytic Leukemia (CLL) leads to progressive accumulation of lymphocytes in the blood, bone marrow, and lymphatic tissues. Previous findings have suggested that the mtDNA could play an important role in CLL. METHODOLOGY/PRINCIPAL FINDINGS The mitochondrial DNA (mtDNA) control-region was analyzed in lymphocyte cell DNA extracts and compared with their granulocyte counterpart extract of 146 patients suffering from B-Cell CLL; B-CLL (all recruited from the Basque country). Major efforts were undertaken to rule out methodological artefacts that would render a high false positive rate for mtDNA instabilities and thus lead to erroneous interpretation of sequence instabilities. Only twenty instabilities were finally confirmed, most of them affecting the homopolymeric stretch located in the second hypervariable segment (HVS-II) around position 310, which is well known to constitute an extreme mutational hotspot of length polymorphism, as these mutations are frequently observed in the general human population. A critical revision of the findings in previous studies indicates a lack of proper methodological standards, which eventually led to an overinterpretation of the role of the mtDNA in CLL tumorigenesis. CONCLUSIONS/SIGNIFICANCE Our results suggest that mtDNA instability is not the primary causal factor in B-CLL. A secondary role of mtDNA mutations cannot be fully ruled out under the hypothesis that the progressive accumulation of mtDNA instabilities could finally contribute to the tumoral process. Recommendations are given that would help to minimize erroneous interpretation of sequencing results in mtDNA studies in tumorigenesis.
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MESH Headings
- Base Sequence
- DNA Primers/genetics
- DNA, Mitochondrial/genetics
- Databases, Genetic
- Granulocytes/cytology
- Haplotypes
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphocytes/cytology
- Models, Statistical
- Molecular Sequence Data
- Mutation
- Phylogeny
- Sequence Analysis, DNA
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | | | - Idoia Martín-Guerrero
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Maite Ardanaz
- Servicio de Hematología, Hospital Txagorritxu, Vitoria, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - África García-Orad
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
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16
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van Asch B, Albarran C, Alonso A, Angulo R, Alves C, Betancor E, Catanesi CI, Corach D, Crespillo M, Doutremepuich C, Estonba A, Fernandes AT, Fernandez E, Garcia AM, Garcia MA, Gilardi P, Gonçalves R, Hernández A, Lima G, Nascimento E, de Pancorbo MM, Parra D, Pinheiro MDF, Prat E, Puente J, Ramírez JL, Rendo F, Rey I, Di Rocco F, Rodríguez A, Sala A, Salla J, Sanchez JJ, Solá D, Silva S, Pestano Brito JJ, Amorim A. Forensic analysis of dog (Canis lupus familiaris) mitochondrial DNA sequences: an inter-laboratory study of the GEP-ISFG working group. Forensic Sci Int Genet 2009; 4:49-54. [PMID: 19948334 DOI: 10.1016/j.fsigen.2009.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 04/20/2009] [Accepted: 04/20/2009] [Indexed: 11/25/2022]
Abstract
A voluntary collaborative exercise aiming at the mitochondrial analysis of canine biological samples was carried out in 2006-2008 by the Non-Human Forensic Genetics Commission of the Spanish and Portuguese Working Group (GEP) of the International Society for Forensic Genetics (ISFG). The participating laboratories were asked to sequence two dog samples (one bloodstain and one hair sample) for the mitochondrial D-loop region comprised between positions 15,372 and 16,083 using suggested primers and PCR conditions, and to compare their results against a reference sequence. Twenty-one participating laboratories reported a total of 67.5% concordant results, 15% non-concordant results, and 17.5% no results. The hair sample analysis presented more difficulty to the participants than the bloodstain analysis, with a high percentage (29%) failing to obtain a result. The high level of participation showed the interest of the community in the analysis of dog forensic samples but the results reveal that crucial methodological issues need to be addressed and further training is required in order to respond proficiently to the demands of forensic casework.
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Affiliation(s)
- Barbara van Asch
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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17
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Álvarez-Iglesias V, Mosquera-Miguel A, Cerezo M, Quintáns B, Zarrabeitia MT, Cuscó I, Lareu MV, García Ó, Pérez-Jurado L, Carracedo Á, Salas A. New population and phylogenetic features of the internal variation within mitochondrial DNA macro-haplogroup R0. PLoS One 2009; 4:e5112. [PMID: 19340307 PMCID: PMC2660437 DOI: 10.1371/journal.pone.0005112] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 03/09/2009] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (approximately 40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies. METHODOLOGY/PRINCIPAL FINDINGS We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (approximately 57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6+/-8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM). CONCLUSIONS/SIGNIFICANCE In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.
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Affiliation(s)
- Vanesa Álvarez-Iglesias
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ana Mosquera-Miguel
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Maria Cerezo
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Beatriz Quintáns
- Fundación Pública Galega de Medicina Xenómica (FPGMX), and Ciber de enfermedades raras (CIBERER), Hospital Clínico Universitario, Universidade de Santiago de Compostela, Galicia, Spain
| | | | - Ivon Cuscó
- Unidad de Genética, Universitat Pompeu Fabra, and U735 CIBER de enfermedades raras (CIBERER), Barcelona, Spain
| | - Maria Victoria Lareu
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | | | - Luis Pérez-Jurado
- Unidad de Genética, Universitat Pompeu Fabra, and U735 CIBER de enfermedades raras (CIBERER), Barcelona, Spain
- Programa de Medicina Molecular y Genética, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX), and Ciber de enfermedades raras (CIBERER), Hospital Clínico Universitario, Universidade de Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
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18
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Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, Comas D, Mitchell RJ, Quintana-Murci L, Tyler-Smith C, Wells RS. The Genographic Project public participation mitochondrial DNA database. PLoS Genet 2007; 3:e104. [PMID: 17604454 PMCID: PMC1904368 DOI: 10.1371/journal.pgen.0030104] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Accepted: 05/11/2007] [Indexed: 11/18/2022] Open
Abstract
The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor-based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.
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Affiliation(s)
- Doron M Behar
- Genomics Research Center, Family Tree DNA, Houston, Texas, United States of America
- Molecular Medicine Laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Saharon Rosset
- Data Analytics Research Group, IBM T. J. Watson Research Center, Yorktown Heights, New York, United States of America
| | - Jason Blue-Smith
- The Genographic Project, National Geographic Society, Washington, District of Columbia, United States of America
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, Russia
| | - Shay Tzur
- Genomics Research Center, Family Tree DNA, Houston, Texas, United States of America
| | - David Comas
- Unitat de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona, Spain
| | - R. John Mitchell
- Department of Genetics, La Trobe University, Bundoora, Australia
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - R. Spencer Wells
- The Genographic Project, National Geographic Society, Washington, District of Columbia, United States of America
- * To whom correspondence should be addressed. E-mail:
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19
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Prieto L, Alonso A, Alves C, Crespillo M, Montesino M, Picornell A, Brehm A, Ramírez JL, Whittle MR, Anjos MJ, Boschi I, Buj J, Cerezo M, Cardoso S, Cicarelli R, Comas D, Corach D, Doutremepuich C, Espinheira RM, Fernández-Fernández I, Filippini S, Garcia-Hirschfeld J, González A, Heinrichs B, Hernández A, Leite FPN, Lizarazo RP, López-Parra AM, López-Soto M, Lorente JA, Mechoso B, Navarro I, Pagano S, Pestano JJ, Puente J, Raimondi E, Rodríguez-Quesada A, Terra-Pinheiro MF, Vidal-Rioja L, Vullo C, Salas A. 2006 GEP-ISFG collaborative exercise on mtDNA: reflections about interpretation, artefacts, and DNA mixtures. Forensic Sci Int Genet 2007; 2:126-33. [PMID: 19083807 DOI: 10.1016/j.fsigen.2007.10.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 09/11/2007] [Accepted: 10/02/2007] [Indexed: 11/29/2022]
Abstract
We report the results of the seventh edition of the GEP-ISFG mitochondrial DNA (mtDNA) collaborative exercise. The samples submitted to the participant laboratories were blood stains from a maternity case and simulated forensic samples, including a case of mixture. The success rate for the blood stains was moderate ( approximately 77%); even though four inexperienced laboratories concentrated about one-third of the total errors. A similar success was obtained for the analysis of mixed samples (78.8% for a hair-saliva mixture and 69.2% for a saliva-saliva mixture). Two laboratories also dissected the haplotypes contributing to the saliva-saliva mixture. Most of the errors were due to reading problems and misinterpretation of electropherograms, demonstrating once more that the lack of a solid devised experimental approach is the main cause of error in mtDNA testing.
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Affiliation(s)
- L Prieto
- Comisaría General de Policía Científica, DNA Laboratory, Madrid, Spain.
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20
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Affiliation(s)
- T A Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196, USA
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Parson W, Dür A. EMPOP--a forensic mtDNA database. Forensic Sci Int Genet 2007; 1:88-92. [PMID: 19083735 DOI: 10.1016/j.fsigen.2007.01.018] [Citation(s) in RCA: 259] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 01/27/2007] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA databases stand as the basis for frequency estimations of mtDNA sequences that became relevant in a case. The establishment of mtDNA databases sounds trivial; however, it has been shown in the past that this undertaking is prone to error for several reasons, particularly human error. We have established a concept for mtDNA data generation, analysis, transfer and quality control that meets forensic standards. Due to the complexity of mtDNA population data tables it is often difficult if not impossible to detect errors, especially for the untrained eye. We developed software based on quasi-median network analysis that visualizes mtDNA data tables and thus signposts sequencing, interpretation and transcription errors. The mtDNA data (N=5173; release 1) are stored and made publicly available via the Internet in the form of the EDNAP mtDNA Population Database, short EMPOP. This website also facilitates quasi-median network analysis and provides results that can be used to check the quality of mtDNA sequence data. EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University Müllerstreet 44, 6020 Innsbruck, Austria.
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22
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Cerný V, Salas A, Hájek M, Zaloudková M, Brdicka R. A bidirectional corridor in the Sahel-Sudan belt and the distinctive features of the Chad Basin populations: a history revealed by the mitochondrial DNA genome. Ann Hum Genet 2007; 71:433-52. [PMID: 17233755 DOI: 10.1111/j.1469-1809.2006.00339.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Chad Basin was sparsely inhabited during the Stone Age, and its continual settlement began with the Holocene. The role played by Lake Chad in the history and migration patterns of Africa is still unclear. We studied the mitochondrial DNA (mtDNA) variability in 448 individuals from 12 ethnically and/or economically (agricultural/pastoral) different populations from Cameroon, Chad, Niger and Nigeria. The data indicate the importance of this region as a corridor connecting East and West Africa; however, this bidirectional flow of people in the Sahel-Sudan Belt did not erase features peculiar to the original Chad Basin populations. A new sub-clade, L3f2, is described, which together with L3e5 is most probably autochthonous in the Chad Basin. The phylogeography of these two sub-haplogroups seems to indicate prehistoric expansion events in the Chad Basin around 28,950 and 11,400 Y.B.P., respectively. The distribution of L3f2 is virtually restricted to the Chad Basin alone, and in particular to Chadic speaking populations, while L3e5 shows evidence for diffusion into North Africa at about 7,100 Y.B.P. The absence of L3f2 and L3e5 in African-Americans, and the limited number of L-haplotypes shared between the Chad Basin populations and African-Americans, indicate the low contribution of the Chad region to the Atlantic slave trade.
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Affiliation(s)
- V Cerný
- Department of Anthropology and Environment, Institute of Archaeology, Czech Academy of Sciences, 118 01 Prague 1, Czech Republic.
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23
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Parson W, Bandelt HJ. Extended guidelines for mtDNA typing of population data in forensic science. Forensic Sci Int Genet 2006; 1:13-9. [PMID: 19083723 DOI: 10.1016/j.fsigen.2006.11.003] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 11/16/2006] [Accepted: 11/19/2006] [Indexed: 10/23/2022]
Abstract
Mitochondrial DNA analysis has become a vital niche in forensic science as it constitutes a powerful technique for low quality and low quantity DNA samples. For the forensic field it is important to employ standardized procedures based on scientific grounds, in order to have mtDNA evidence be accepted in court. Here, we modify and extend recommendations that were spelled out previously in the absence of solid knowledge about the worldwide phylogeny. Refinement of those earlier guidelines became necessary in regard to sample selection, amplification and sequencing strategies, as well as a posteriori quality control of mtDNA profiles. The notation of sequence data should thus reflect this growing knowledge.
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Affiliation(s)
- Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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Alvarez-Iglesias V, Jaime JC, Carracedo A, Salas A. Coding region mitochondrial DNA SNPs: targeting East Asian and Native American haplogroups. Forensic Sci Int Genet 2006; 1:44-55. [PMID: 19083727 DOI: 10.1016/j.fsigen.2006.09.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 09/15/2006] [Accepted: 09/17/2006] [Indexed: 11/30/2022]
Abstract
We have developed a single PCR multiplex SNaPshot reaction that consists of 32 coding region SNPs that allows (i) increasing the discrimination power of the mitochondrial DNA (mtDNA) typing in forensic casework, and (ii) haplogroup assignments of mtDNA profiles in both human population studies (e.g. anthropological) and medical research. The selected SNPs target the East Asian phylogeny, including its Native American derived branches. We have validated this multiplex assay by genotyping a sample of East Asians (Taiwanese) and Native Americans (Argentineans). In addition to the coding SNP typing, we have sequenced the complete control region for the same samples. The genotyping results (control region plus SNaPshot profiles) are in good agreement with previous human population genetic studies (based on e.g. complete sequencing) and the known mtDNA phylogeny. We observe that the SNaPshot method is reliable, rapid, and cost effective in comparison with other techniques of multiplex SNP genotyping. We discuss the advantages of our SNP genotyping selection with respect to previous attempts, and we highlight the importance of using the known mtDNA phylogeny as a framework for SNP profile interpretation and as a tool to minimize genotyping errors.
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Affiliation(s)
- V Alvarez-Iglesias
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
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Montesino M, Salas A, Crespillo M, Albarrán C, Alonso A, Alvarez-Iglesias V, Cano JA, Carvalho M, Corach D, Cruz C, Di Lonardo A, Espinheira R, Farfán MJ, Filippini S, García-Hirschfeld J, Hernández A, Lima G, López-Cubría CM, López-Soto M, Pagano S, Paredes M, Pinheiro MF, Rodríguez-Monge AM, Sala A, Sóñora S, Sumita DR, Vide MC, Whittle MR, Zurita A, Prieto L. Analysis of body fluid mixtures by mtDNA sequencing: An inter-laboratory study of the GEP-ISFG working group. Forensic Sci Int 2006; 168:42-56. [PMID: 16899347 DOI: 10.1016/j.forsciint.2006.06.066] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2006] [Revised: 06/15/2006] [Accepted: 06/17/2006] [Indexed: 10/24/2022]
Abstract
The mitochondrial DNA (mtDNA) working group of the GEP-ISFG (Spanish and Portuguese Group of the International Society for Forensic Genetics) carried out an inter-laboratory exercise consisting of the analysis of mtDNA sequencing patterns in mixed stains (saliva/semen and blood/semen). Mixtures were prepared with saliva or blood from a female donor and three different semen dilutions (pure, 1:10 and 1:20) in order to simulate forensic casework. All labs extracted the DNA by preferential lysis and amplified and sequenced the first mtDNA hypervariable region (HVS-I). Autosomal and Y-STR markers were also analysed in order to compare nuclear and mitochondrial results from the same DNA extracts. A mixed stain prepared using semen from a vasectomized individual was also analysed. The results were reasonably consistent among labs for the first fractions but not for the second ones, for which some laboratories reported contamination problems. In the first fractions, both the female and male haplotypes were generally detected in those samples prepared with undiluted semen. In contrast, most of the mixtures prepared with diluted semen only yielded the female haplotype, suggesting that the mtDNA copy number per cell is smaller in semen than in saliva or blood. Although the detection level of the male component decreased in accordance with the degree of semen dilution, it was found that the loss of signal was not consistently uniform throughout each electropherogram. Moreover, differences between mixtures prepared from different donors and different body fluids were also observed. We conclude that the particular characteristics of each mixed stain can deeply influence the interpretation of the mtDNA evidence in forensic mixtures (leading in some cases to false exclusions). In this sense, the implementation of preliminary tests with the aim of identifying the fluids involved in the mixture is an essential tool. In addition, in order to prevent incorrect conclusions in the interpretation of electropherograms we strongly recommend: (i) the use of additional sequencing primers to confirm the sequencing results and (ii) interpreting the results to the light of the phylogenetic perspective.
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26
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Brandstätter A, Klein R, Duftner N, Wiegand P, Parson W. Application of a quasi-median network analysis for the visualization of character conflicts to a population sample of mitochondrial DNA control region sequences from southern Germany (Ulm). Int J Legal Med 2006; 120:310-4. [PMID: 16871406 DOI: 10.1007/s00414-006-0114-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 06/12/2006] [Indexed: 11/28/2022]
Abstract
Entire mtDNA control region sequences from 100 individuals in a west Eurasian population sample from southern Germany (around the city of Ulm) were generated and analyzed. The control region was amplified in one piece and sequenced with ten different sequencing primers. Sequence evaluation was performed independently. Phylogenetic analyses were used for quality assurance purposes and for the determination of the haplogroup affiliation of the samples. The sequences were scrutinized performing a quasi-median network analysis. To visualize character conflicts, frequent mutations were filtered, and the reduced data were represented by the torso of their quasi-median network. Character incompatibilities were found to be based on real biological patterns of homoplasy. The population data will be incorporated in the EMPOP database ( http://www.empop.org ).
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Affiliation(s)
- Anita Brandstätter
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, Innsbruck, 6020, Austria
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Brandstätter A, Niederstätter H, Pavlic M, Grubwieser P, Parson W. Generating population data for the EMPOP database - an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example. Forensic Sci Int 2006; 166:164-75. [PMID: 16829006 DOI: 10.1016/j.forsciint.2006.05.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 05/09/2006] [Accepted: 05/09/2006] [Indexed: 11/27/2022]
Abstract
The European DNA profiling group (EDNAP) mtDNA population database (EMPOP) is an international collaborative project between DNA laboratories performing mtDNA analysis and the DNA laboratory of the Institute of Legal Medicine (GMI) in Innsbruck, Austria. The goal is to set up a directly accessible mtDNA population database, which can be used in routine forensic casework for frequency investigations. Here we describe a safe laboratory scheme involving electronical data handling and computer-aided data transfer, which help to minimize errors originating from potential sample mix-up, data misinterpretation and incorrect transcription. The procedure is demonstrated by example of an mtDNA control region population study on 273 unrelated individuals from Austria. Our population sample was compared with five other European populations via an analysis of molecular variance (AMOVA). The inclusion of regions outside HVS-I and HVS-II increased the amount of information on the haplogroup diagnostic sites in the control region. Most of the haplotypes in Austrians fell into haplogroups H, J, K, T, and U. The random match probability in Austrians was 1:125; the average number of nucleotide differences between individuals in the Austrian database was 9.32.
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Affiliation(s)
- Anita Brandstätter
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstr. 44, 6020 Innsbruck, Austria
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28
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Crespillo M, Paredes MR, Prieto L, Montesino M, Salas A, Albarran C, Alvarez-Iglesias V, Amorin A, Berniell-Lee G, Brehm A, Carril JC, Corach D, Cuevas N, Di Lonardo AM, Doutremepuich C, Espinheira RM, Espinoza M, Gómez F, González A, Hernández A, Hidalgo M, Jimenez M, Leite FPN, López AM, López-Soto M, Lorente JA, Pagano S, Palacio AM, Pestano JJ, Pinheiro MF, Raimondi E, Ramón MM, Tovar F, Vidal-Rioja L, Vide MC, Whittle MR, Yunis JJ, Garcia-Hirschfel J. Results of the 2003–2004 GEP-ISFG collaborative study on mitochondrial DNA: Focus on the mtDNA profile of a mixed semen-saliva stain. Forensic Sci Int 2006; 160:157-67. [PMID: 16243467 DOI: 10.1016/j.forsciint.2005.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Revised: 09/17/2005] [Accepted: 09/17/2005] [Indexed: 11/29/2022]
Abstract
We report here a review of the seventh mitochondrial DNA (mtDNA) exercise undertaken by the Spanish and Portuguese working group (GEP) of the International Society for Forensic Genetics (ISFG) corresponding to the period 2003-2004. Five reference bloodstains from five donors (M1-M5), a mixed stain of saliva and semen (M6), and a hair sample (M7) were submitted to each participating laboratory for nuclear DNA (nDNA; autosomal STR and Y-STR) and mtDNA analysis. Laboratories were asked to investigate the contributors of samples M6 and M7 among the reference donors (M1-M5). A total of 34 laboratories reported total or partial mtDNA sequence data from both, the reference bloodstains (M1-M5) and the hair sample (M7) concluding a match between mtDNA profiles of M5 and M7. Autosomal STR and Y-STR profiling was the preferred strategy to investigate the contributors of the semen/saliva mixture (M6). Nuclear DNA profiles were consistent with a mixture of saliva from the donor (female) of M4 and semen from donor M5, being the semen (XY) profile the dominant component of the mixture. Strikingly, and in contradiction to the nuclear DNA analysis, mtDNA sequencing results yield a more simple result: only the saliva contribution (M4) was detected, either after preferential lysis or after complete DNA digestion. Some labs provided with several explanations for this finding and carried out additional experiments to explain this apparent contradictory result. The results pointed to the existence of different relative amounts of nuclear and mtDNAs in saliva and semen. We conclude that this circumstance could strongly influence the interpretation of the mtDNA evidence in unbalanced mixtures and in consequence lead to false exclusions. During the GEP-ISFG annual conference a validation study was planned to progress in the interpretation of mtDNA from different mixtures.
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Affiliation(s)
- Manuel Crespillo
- Instituto Nacional de Toxicología y Ciencias Forenses, Servicio de Biología, Barcelona, Spain.
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29
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Salas A, Bandelt HJ, Macaulay V, Richards MB. Phylogeographic investigations: the role of trees in forensic genetics. Forensic Sci Int 2006; 168:1-13. [PMID: 16814504 DOI: 10.1016/j.forsciint.2006.05.037] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 05/19/2006] [Accepted: 05/21/2006] [Indexed: 11/16/2022]
Abstract
The human mitochondrial DNA (mtDNA) genome is commonly analyzed in various disciplines, such as population, medical, and forensic genetics, but conceptual and scientific exchange between them is still limited. Here we review several aspects of the mtDNA phylogeny that are particularly--but not exclusively--of interest to the forensic community. Among the issues that arise, we emphasize the importance of integrating evolutionary concepts into the forensic routine. We also discuss topics such as mtDNA mutation-rate heterogeneity and the weight of evidence, ethnic affiliations of mtDNA profiles, and the abuse of reference databases. Finally, we show the usefulness of coding-region variation in a forensic context.
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Affiliation(s)
- A Salas
- Unidad de Genética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, 15782 Galicia, Spain.
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Brandstätter A, Sänger T, Lutz-Bonengel S, Parson W, Béraud-Colomb E, Wen B, Kong QP, Bravi CM, Bandelt HJ. Phantom mutation hotspots in human mitochondrial DNA. Electrophoresis 2005; 26:3414-29. [PMID: 16167362 DOI: 10.1002/elps.200500307] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.
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Affiliation(s)
- Anita Brandstätter
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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31
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Salas A, Carracedo A, Macaulay V, Richards M, Bandelt HJ. A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics. Biochem Biophys Res Commun 2005; 335:891-9. [PMID: 16102729 DOI: 10.1016/j.bbrc.2005.07.161] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 07/27/2005] [Indexed: 11/19/2022]
Abstract
Several suggestions have been made for avoiding errors in mitochondrial DNA (mtDNA) sequencing and documentation. Unfortunately, the current clinical, forensic, and population genetic literature on mtDNA still delivers a large number of studies with flawed sequence data, which, in extreme cases, damage the whole message of a study. The phylogenetic approach has been shown to be useful for pinpointing most of the errors. However, many geneticists, especially in the forensic and medical fields, are not familiar with either effective search strategies or the evolutionary terminology. We here provide a manual that should help prevent errors at any stage by re-examining data fresh from the sequencer in the light of previously published data. A fictitious case study of a European mtDNA data set (albeit composed from the literature) then demonstrates the steps one has to go through in order to assess the quality of sequencing and documentation.
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Affiliation(s)
- Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultade de Medicina, 15782 Universidade de Santiago de Compostela, Centro Nacional de Xenotipado (CeGen), Hospital Clínico Universitario, 15706 Galicia, Spain.
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