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Freire-Aradas A, Tomsia M, Piniewska-Róg D, Ambroa-Conde A, Casares de Cal MA, Pisarek A, Gómez-Tato A, Álvarez-Dios J, Pośpiech E, Parson W, Kayser M, Phillips C, Branicki W. Development of an epigenetic age predictor for costal cartilage with a simultaneous somatic tissue differentiation system. Forensic Sci Int Genet 2023; 67:102936. [PMID: 37783021 DOI: 10.1016/j.fsigen.2023.102936] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/14/2023] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 10/04/2023]
Abstract
Age prediction from DNA has been a topic of interest in recent years due to the promising results obtained when using epigenetic markers. Since DNA methylation gradually changes across the individual's lifetime, prediction models have been developed accordingly for age estimation. The tissue-dependence for this biomarker usually necessitates the development of tissue-specific age prediction models, in this way, multiple models for age inference have been constructed for the most commonly encountered forensic tissues (blood, oral mucosa, semen). The analysis of skeletal remains has also been attempted and prediction models for bone have now been reported. Recently, the VISAGE Enhanced Tool was developed for the simultaneous DNA methylation analysis of 8 age-correlated loci using targeted high-throughput sequencing. It has been shown that this method is compatible with epigenetic age estimation models for blood, buccal cells, and bone. Since when dealing with decomposed cadavers or postmortem samples, cartilage samples are also an important biological source, an age prediction model for cartilage has been generated in the present study based on methylation data collected using the VISAGE Enhanced Tool. In this way, we have developed a forensic cartilage age prediction model using a training set composed of 109 samples (19-74 age range) based on DNA methylation levels from three CpGs in FHL2, TRIM59 and KLF14, using multivariate quantile regression which provides a mean absolute error (MAE) of ± 4.41 years. An independent testing set composed of 72 samples (19-75 age range) was also analyzed and provided an MAE of ± 4.26 years. In addition, we demonstrate that the 8 VISAGE markers, comprising EDARADD, TRIM59, ELOVL2, MIR29B2CHG, PDE4C, ASPA, FHL2 and KLF14, can be used as tissue prediction markers which provide reliable blood, buccal cells, bone, and cartilage differentiation using a developed multinomial logistic regression model. A training set composed of 392 samples (n = 87 blood, n = 86 buccal cells, n = 110 bone and n = 109 cartilage) was used for building the model (correct classifications: 98.72%, sensitivity: 0.988, specificity: 0.996) and validation was performed using a testing set composed of 192 samples (n = 38 blood, n = 36 buccal cells, n = 46 bone and n = 72 cartilage) showing similar predictive success to the training set (correct classifications: 97.4%, sensitivity: 0.968, specificity: 0.991). By developing both a new cartilage age model and a tissue differentiation model, our study significantly expands the use of the VISAGE Enhanced Tool while increasing the amount of DNA methylation-based information obtained from a single sample and a single forensic laboratory analysis. Both models have been placed in the open-access Snipper forensic classification website.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
| | - M Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Medical University of Silesia, Katowice, Poland
| | - D Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - M A Casares de Cal
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - A Pisarek
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - A Gómez-Tato
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Poland
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Austria; Forensic Science Program, Pennsylvania State University, PA, USA
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - W Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland; Institute of Forensic Research, Kraków, Poland.
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2
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Ruiz-Ramírez J, de la Puente M, Xavier C, Ambroa-Conde A, Álvarez-Dios J, Freire-Aradas A, Mosquera-Miguel A, Ralf A, Amory C, Katsara MA, Khellaf T, Nothnagel M, Cheung EYY, Gross TE, Schneider PM, Uacyisrael J, Oliveira S, Klautau-Guimarães MDN, Carvalho-Gontijo C, Pośpiech E, Branicki W, Parson W, Kayser M, Carracedo A, Lareu MV, Phillips C. Development and evaluations of the ancestry informative markers of the VISAGE Enhanced Tool for Appearance and Ancestry. Forensic Sci Int Genet 2023; 64:102853. [PMID: 36917866 DOI: 10.1016/j.fsigen.2023.102853] [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: 06/03/2022] [Revised: 02/15/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
The VISAGE Enhanced Tool for Appearance and Ancestry (ET) has been designed to combine markers for the prediction of bio-geographical ancestry plus a range of externally visible characteristics into a single massively parallel sequencing (MPS) assay. We describe the development of the ancestry panel markers used in ET, and the enhanced analyses they provide compared to previous MPS-based forensic ancestry assays. As well as established autosomal single nucleotide polymorphisms (SNPs) that differentiate sub-Saharan African, European, East Asian, South Asian, Native American, and Oceanian populations, ET includes autosomal SNPs able to efficiently differentiate populations from Middle East regions. The ability of the ET autosomal ancestry SNPs to distinguish Middle East populations from other continentally defined population groups is such that characteristic patterns for this region can be discerned in genetic cluster analysis using STRUCTURE. Joint cluster membership estimates showing individual co-ancestry that signals North African or East African origins were detected, or cluster patterns were seen that indicate origins from central and Eastern regions of the Middle East. In addition to an augmented panel of autosomal SNPs, ET includes panels of 85 Y-SNPs, 16 X-SNPs and 21 autosomal Microhaplotypes. The Y- and X-SNPs provide a distinct method for obtaining extra detail about co-ancestry patterns identified in males with admixed backgrounds. This study used the 1000 Genomes admixed African and admixed American sample sets to fully explore these enhancements to the analysis of individual co-ancestry. Samples from urban and rural Brazil with contrasting distributions of African, European, and Native American co-ancestry were also studied to gauge the efficiency of combining Y- and X-SNP data for this purpose. The small panel of Microhaplotypes incorporated in ET were selected because they showed the highest levels of haplotype diversity amongst the seven population groups we sought to differentiate. Microhaplotype data was not formally combined with single-site SNP genotypes to analyse ancestry. However, the haplotype sequence reads obtained with ET from these loci creates an effective system for de-convoluting two-contributor mixed DNA. We made simple mixture experiments to demonstrate that when the contributors have different ancestries and the mixture ratios are imbalanced (i.e., not 1:1 mixtures) the ET Microhaplotype panel is an informative system to infer ancestry when this differs between the contributors.
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Affiliation(s)
- J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - C Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, 15705 Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, 3015 CN Rotterdam, South Holland, the Netherlands
| | - C Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - M A Katsara
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany
| | - T Khellaf
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany
| | - M Nothnagel
- Cologne Center for Genomics, University of Cologne, 50823 Cologne, Germany; University Hospital Cologne, 50937 Cologne, Germany
| | - E Y Y Cheung
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine and University Clinic, University of Cologne, 50823 Cologne, Germany
| | - J Uacyisrael
- Fiji Police Forensic Biology and DNA Laboratory, Nasova, Suva, Fiji
| | - S Oliveira
- Departamento Genética e Morfologia, Universidade de Brasília, Brasília, DF, Brazil
| | | | - C Carvalho-Gontijo
- Departamento Genética e Morfologia, Universidade de Brasília, Brasília, DF, Brazil
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - W Branicki
- Institute of Zoology and Biomedical Research, Jagiellonian University, 30-387 Kraków, Poland
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - M Kayser
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, 3015 CN Rotterdam, South Holland, the Netherlands
| | - A Carracedo
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Instituto de Investigación Sanitaria (IDIS),15706 Santiago de Compostela, Spain; Genomics Group, CIBERER, CIMUS, University of Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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3
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Freire-Aradas A, Girón-Santamaría L, Mosquera-Miguel A, Ambroa-Conde A, Phillips C, Casares de Cal M, Gómez-Tato A, Álvarez-Dios J, Pospiech E, Aliferi A, Syndercombe Court D, Branicki W, Lareu M. A common epigenetic clock from childhood to old age. Forensic Sci Int Genet 2022; 60:102743. [DOI: 10.1016/j.fsigen.2022.102743] [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] [Received: 12/21/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
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Heidegger A, Pisarek A, de la Puente M, Niederstätter H, Pośpiech E, Woźniak A, Schury N, Unterländer M, Sidstedt M, Junker K, Ventayol Garcia M, Laurent FX, Ulus A, Vannier J, Bastisch I, Hedman J, Sijen T, Branicki W, Xavier C, Parson W. Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis. Forensic Sci Int Genet 2021; 56:102596. [PMID: 34763164 DOI: 10.1016/j.fsigen.2021.102596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022]
Abstract
The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority from blood. Age prediction from semen requires different DNA methylation markers and the only assays currently developed for forensic analysis are based on SNaPshot or pyrosequencing. Here, we describe a new assay using massively parallel sequencing to analyse 13 candidate CpG sites targeted in two multiplex PCRs. The assay has been validated by five consortium laboratories of the VISible Attributes through GEnomics (VISAGE) project within a collaborative exercise and was tested for reproducible quantification of DNA methylation levels and sensitivity with DNA methylation controls. Furthermore, DNA extracts and stains on Whatman FTA cards from two semen samples were used to evaluate concordance and mimic casework samples. Overall, the assay yielded high read depths (> 1000 reads) at all 13 marker positions. The methylation values obtained indicated robust quantification with an average standard deviation of 2.8% at the expected methylation level of 50% across the 13 markers and a good performance with 50 ng DNA input into bisulfite conversion. The absolute difference of quantifications from one participating laboratory to the mean quantifications of concordance and semen stains of remaining laboratories was approximately 1%. These results demonstrated the assay to be robust and suitable for age estimation from semen in forensic investigations. In addition to the 13-marker assay, a more streamlined protocol combining only five age markers in one multiplex PCR was developed. Preliminary results showed no substantial differences in DNA methylation quantification between the two assays, indicating its applicability with the VISAGE age model for semen developed with data from the complete 13-marker tool.
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Affiliation(s)
- A Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - A Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - M de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - H Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - A Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - N Schury
- Federal Criminal Police Office, Wiesbaden, Germany
| | | | - M Sidstedt
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - K Junker
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - M Ventayol Garcia
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | - F X Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - A Ulus
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - J Vannier
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - I Bastisch
- Federal Criminal Police Office, Wiesbaden, Germany
| | - J Hedman
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - T Sijen
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands; University of Amsterdam, Swammerdam Institute of Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Central Forensic Laboratory of the Police, Warsaw, Poland
| | - C Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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5
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Freire-Aradas A, Pośpiech E, Aliferi A, Girón-Santamaría L, Mosquera-Miguel A, Pisarek A, Ambroa-Conde A, Phillips C, Casares de Cal MA, Gómez-Tato A, Spólnicka M, Woźniak A, Álvarez-Dios J, Ballard D, Court DS, Branicki W, Carracedo Á, Lareu MV. A Comparison of Forensic Age Prediction Models Using Data From Four DNA Methylation Technologies. Front Genet 2020; 11:932. [PMID: 32973877 PMCID: PMC7466768 DOI: 10.3389/fgene.2020.00932] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 04/29/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Individual age estimation can be applied to criminal, legal, and anthropological investigations. DNA methylation has been established as the biomarker of choice for age prediction, since it was observed that specific CpG positions in the genome show systematic changes during an individual’s lifetime, with progressive increases or decreases in methylation levels. Subsequently, several forensic age prediction models have been reported, providing average age prediction error ranges of ±3–4 years, using a broad spectrum of technologies and underlying statistical analyses. DNA methylation assessment is not categorical but quantitative. Therefore, the detection platform used plays a pivotal role, since quantitative and semi-quantitative technologies could potentially result in differences in detected DNA methylation levels. In the present study, we analyzed as a shared sample pool, 84 blood-based DNA controls ranging from 18 to 99 years old using four different technologies: EpiTYPER®, pyrosequencing, MiSeq, and SNaPshotTM. The DNA methylation levels detected for CpG sites from ELOVL2, FHL2, and MIR29B2 with each system were compared. A restricted three CpG-site age prediction model was rebuilt for each system, as well as for a combination of technologies, based on previous training datasets, and age predictions were calculated accordingly for all the samples detected with the previous technologies. While the DNA methylation patterns and subsequent age predictions from EpiTYPER®, pyrosequencing, and MiSeq systems are largely comparable for the CpG sites studied, SNaPshotTM gives bigger differences reflected in higher predictive errors. However, these differences can be reduced by applying a z-score data transformation.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - A Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - L Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - A Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - M A Casares de Cal
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - A Gómez-Tato
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - M Spólnicka
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - A Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Galicia, Spain
| | - D Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - D Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.,Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ángel Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.,Fundación Pública Galega de Medicina Xenómica - CIBERER-IDIS, Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
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6
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Ingold S, Dørum G, Hanson E, Berti A, Branicki W, Brito P, Elsmore P, Gettings K, Giangasparo F, Gross T, Hansen S, Hanssen E, Kampmann ML, Kayser M, Laurent FX, Morling N, Mosquera-Miguel A, Parson W, Phillips C, Porto M, Pośpiech E, Roeder A, Schneider P, Schulze Johann K, Steffen C, Syndercombe-Court D, Trautmann M, van den Berge M, van der Gaag K, Vannier J, Verdoliva V, Vidaki A, Xavier C, Ballantyne J, Haas C. Body fluid identification using a targeted mRNA massively parallel sequencing approach – results of a EUROFORGEN/EDNAP collaborative exercise. Forensic Sci Int Genet 2018; 34:105-115. [DOI: 10.1016/j.fsigen.2018.01.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 01/05/2018] [Indexed: 11/30/2022]
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7
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Freire-Aradas A, Phillips C, Mosquera-Miguel A, Girón-Santamaría L, Gómez-Tato A, Casares de Cal M, Álvarez-Dios J, Ansede-Bermejo J, Torres-Español M, Schneider PM, Pośpiech E, Branicki W, Carracedo Á, Lareu MV. Development of a methylation marker set for forensic age estimation using analysis of public methylation data and the Agena Bioscience EpiTYPER system. Forensic Sci Int Genet 2016; 24:65-74. [PMID: 27337627 DOI: 10.1016/j.fsigen.2016.06.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [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: 04/25/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 01/24/2023]
Abstract
Individual age estimation has the potential to provide key information that could enhance and extend DNA intelligence tools. Following predictive tests for externally visible characteristics developed in recent years, prediction of age could guide police investigations and improve the assessment of age-related phenotype expression patterns such as hair colour changes and early onset of male pattern baldness. DNA methylation at CpG positions has emerged as the most promising DNA tests to ascertain the individual age of the donor of a biological contact trace. Although different methodologies are available to detect DNA methylation, EpiTYPER technology (Agena Bioscience, formerly Sequenom) provides useful characteristics that can be applied as a discovery tool in localized regions of the genome. In our study, a total of twenty-two candidate genomic regions, selected from the assessment of publically available data from the Illumina HumanMethylation 450 BeadChip, had a total of 177 CpG sites with informative methylation patterns that were subsequently investigated in detail. From the methylation analyses made, a novel age prediction model based on a multivariate quantile regression analysis was built using the seven highest age-correlated loci of ELOVL2, ASPA, PDE4C, FHL2, CCDC102B, C1orf132 and chr16:85395429. The detected methylation levels in these loci provide a median absolute age prediction error of ±3.07years and a percentage of prediction error relative to the age of 6.3%. We report the predictive performance of the developed model using cross validation of a carefully age-graded training set of 725 European individuals and a test set of 52 monozygotic twin pairs. The multivariate quantile regression age predictor, using the CpG sites selected in this study, has been placed in the open-access Snipper forensic classification website.
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Affiliation(s)
- A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - L Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Gómez-Tato
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - M Casares de Cal
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - J Álvarez-Dios
- Faculty of Mathematics, University of Santiago de Compostela, Spain
| | - J Ansede-Bermejo
- Spanish National Genotyping Center-USC-PRB2-ISCIII, Santiago de Compostela, Spain
| | - M Torres-Español
- Spanish National Genotyping Center-USC-PRB2-ISCIII, Santiago de Compostela, Spain
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - E Pośpiech
- Institute of Zoology, Faculty of Biology and Earth Sciences, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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8
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Tagliabue E, Fargnoli MC, Gandini S, Maisonneuve P, Liu F, Kayser M, Nijsten T, Han J, Kumar R, Gruis NA, Ferrucci L, Branicki W, Dwyer T, Blizzard L, Helsing P, Autier P, García-Borrón JC, Kanetsky PA, Landi MT, Little J, Newton-Bishop J, Sera F, Raimondi S. MC1R gene variants and non-melanoma skin cancer: a pooled-analysis from the M-SKIP project. Br J Cancer 2015; 113:354-63. [PMID: 26103569 PMCID: PMC4506395 DOI: 10.1038/bjc.2015.231] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 02/16/2015] [Revised: 05/18/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The melanocortin-1-receptor (MC1R) gene regulates human pigmentation and is highly polymorphic in populations of European origins. The aims of this study were to evaluate the association between MC1R variants and the risk of non-melanoma skin cancer (NMSC), and to investigate whether risk estimates differed by phenotypic characteristics. METHODS Data on 3527 NMSC cases and 9391 controls were gathered through the M-SKIP Project, an international pooled-analysis on MC1R, skin cancer and phenotypic characteristics. We calculated summary odds ratios (SOR) with random-effect models, and performed stratified analyses. RESULTS Subjects carrying at least one MC1R variant had an increased risk of NMSC overall, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC): SOR (95%CI) were 1.48 (1.24-1.76), 1.39 (1.15-1.69) and 1.61 (1.35-1.91), respectively. All of the investigated variants showed positive associations with NMSC, with consistent significant results obtained for V60L, D84E, V92M, R151C, R160W, R163Q and D294H: SOR (95%CI) ranged from 1.42 (1.19-1.70) for V60L to 2.66 (1.06-6.65) for D84E variant. In stratified analysis, there was no consistent pattern of association between MC1R and NMSC by skin type, but we consistently observed higher SORs for subjects without red hair. CONCLUSIONS Our pooled-analysis highlighted a role of MC1R variants in NMSC development and suggested an effect modification by red hair colour phenotype.
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Affiliation(s)
- E Tagliabue
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Via Ripamonti 435, Milan 20141, Italy
| | - M C Fargnoli
- Department of Dermatology, University of L'Aquila, 47100 L'Aquila, Italy
| | - S Gandini
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Via Ripamonti 435, Milan 20141, Italy
| | - P Maisonneuve
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Via Ripamonti 435, Milan 20141, Italy
| | - F Liu
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, 3000 DR Rotterdam, The Netherlands
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center, 3000 DR Rotterdam, The Netherlands
| | - T Nijsten
- Department of Dermatology, Erasmus MC University Medical Center, 3000 DR Rotterdam, The Netherlands
| | - J Han
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - R Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, D-69120 Heidelberg, Germany
| | - N A Gruis
- Department of Dermatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - L Ferrucci
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale Cancer Center, New Haven, CT 06520-8034, USA
| | - W Branicki
- Institute of Forensic Research, 31-033 Krakow, Poland
| | - T Dwyer
- Murdoch Childrens Research Institute, Royal Children's Hospital, Victoria 3052, Australia
| | - L Blizzard
- Menzies Research Institute Tasmania, University of Tasmania, Hobart, 7001 Australia
| | - P Helsing
- Department of Pathology, Oslo University Hospital, N-0027 Oslo, Norway
| | - P Autier
- International Prevention Research Institute, Lyon 69006, France
| | - J C García-Borrón
- Department of Biochemistry, Molecular Biology and Immunology, University of Murcia, 30100 Murcia, Spain
| | - P A Kanetsky
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - M T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD 20892-7236, USA
| | - J Little
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada ON K1N 6N5
| | - J Newton-Bishop
- Section of Epidemiology and Biostatistics, Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | - F Sera
- UCL Institute of Child Health, London WC1N 1EH, UK
| | - S Raimondi
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Via Ripamonti 435, Milan 20141, Italy
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9
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Santos C, Fondevila M, Ballard D, Banemann R, Bento AM, Børsting C, Branicki W, Brisighelli F, Burrington M, Capal T, Chaitanya L, Daniel R, Decroyer V, England R, Gettings KB, Gross TE, Haas C, Harteveld J, Hoff-Olsen P, Hoffmann A, Kayser M, Kohler P, Linacre A, Mayr-Eduardoff M, McGovern C, Morling N, O'Donnell G, Parson W, Pascali VL, Porto MJ, Roseth A, Schneider PM, Sijen T, Stenzl V, Court DS, Templeton JE, Turanska M, Vallone PM, Oorschot RAHV, Zatkalikova L, Carracedo Á, Phillips C. Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise. Forensic Sci Int Genet 2015; 19:56-67. [PMID: 26122263 DOI: 10.1016/j.fsigen.2015.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [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: 01/21/2015] [Revised: 05/06/2015] [Accepted: 06/09/2015] [Indexed: 10/23/2022]
Abstract
There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.
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Affiliation(s)
- C Santos
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - M Fondevila
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - D Ballard
- Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK
| | - R Banemann
- Federal Criminal Police Office, Wiesbaden, Germany
| | - A M Bento
- Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - C Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark
| | - W Branicki
- Section of Forensic Genetics, Institute of Forensic Research, Kraków, Poland
| | - F Brisighelli
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - T Capal
- Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - L Chaitanya
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - R Daniel
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia
| | - V Decroyer
- National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium
| | - R England
- ESR, Private Bag 92021, Auckland, New Zealand
| | - K B Gettings
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - T E Gross
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - C Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - J Harteveld
- Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands
| | - P Hoff-Olsen
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - A Hoffmann
- Federal Criminal Police Office, Wiesbaden, Germany
| | - M Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - P Kohler
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - A Linacre
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia
| | - M Mayr-Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - C McGovern
- ESR, Private Bag 92021, Auckland, New Zealand
| | - N Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen, Denmark; National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, Brussels, Belgium
| | - G O'Donnell
- Forensic Science Laboratory, Dublin, Ireland
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - V L Pascali
- Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - M J Porto
- Forensic Genetic and Biology Service, Centre Branch, National Institute of Legal Medicine and Forensic Sciences, Coimbra, Portugal
| | - A Roseth
- Department of Forensic Biology, Norwegian Institute of Public Health, Oslo, Norway
| | - P M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - T Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, The Hague, The Netherlands
| | - V Stenzl
- Department of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
| | - D Syndercombe Court
- Department of Forensic and Analytical Science, Faculty of Life Science, King's College London, UK
| | - J E Templeton
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5042, Australia
| | - M Turanska
- Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia
| | - P M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - R A H van Oorschot
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia
| | - L Zatkalikova
- Institute of Forensic Science, Ministry of the Interior, Department of Biology and DNA Analysis, Slovenská Lupca, Slovakia
| | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
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10
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Branicki W, Szczerbińska A, Brudnik U, Wolańska-Nowak P, Kupiec T. The OCA2 gene as a marker for eye colour prediction. Forensic Science International: Genetics Supplement Series 2008. [DOI: 10.1016/j.fsigss.2007.10.062] [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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11
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Branicki W, Brudnik U, Kupiec T, Wolańska-Nowak P, Szczerbińska A, Wojas-Pelc A. Association of polymorphic sites in the OCA2 gene with eye colour using the tree scanning method. Ann Hum Genet 2007; 72:184-92. [PMID: 18093281 DOI: 10.1111/j.1469-1809.2007.00407.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A number of genes are considered to affect normal variation in human pigmentation. Recent studies have indicated that OCA2 is the crucial gene involved in the high variation of iris colour present among populations of European descent. In this study, eleven polymorphisms of the OCA2 gene were examined in search of their association with different pigment traits. The evolutionary tree scanning method indicated that the strongest phenotypic eye colour variation is associated with the branch defined by nonsynonymous change rs1800407, which refers to amino acid causing change Arg419Gln located in exon 13. Single SNP analysis indicated that allele 419Gln is associated with green/hazel iris colour (p < 0.001). According to tree scanning analysis, the proportion of eye colour variation explained by this nucleotide position is merely 4%. Thus, additional variation present in the OCA2 gene and perhaps some other pigment related genes must be taken into account in order to explain the high phenotypic variation in iris colour.
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Affiliation(s)
- W Branicki
- Institute of Forensic Research, Section of Forensic Genetics, Westerplatte 9, Krakow, Poland.
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12
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Babik W, Branicki W, Crnobrnja-Isailović J, Cogălniceanu D, Sas I, Olgun K, Poyarkov NA, Garcia-París M, Arntzen JW. Phylogeography of two European newt species--discordance between mtDNA and morphology. Mol Ecol 2005; 14:2475-91. [PMID: 15969729 DOI: 10.1111/j.1365-294x.2005.02605.x] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The newts Triturus vulgaris and Triturus montandoni are sister species that exhibit contrasting levels of intraspecific morphological variation. Triturus vulgaris has a broad Eurasiatic distribution encompassing both formerly glaciated and unglaciated areas and shows substantial morphological differentiation in the southern part of its range, while T. montandoni, confined to the Carpathians, is morphologically uniform. We analysed sequence variation of two mtDNA fragments of the total length of c. 1850 bp in 285 individuals of both species collected from 103 localities. Phylogenetic analysis of 200 unique haplotypes defined 12 major clades, their age estimated at c. 4.5-1.0 million years (Myr). Most of the older clades were found in the southern part of the range, and also in central Europe, mainly in Romania. The distribution of mtDNA clades points to the existence of several glacial refugia, located in the Caucasus region, Anatolia, the Balkan Peninsula, Italy, and more to the north in central Europe. The concordance between mtDNA based phylogeny and the distribution of T. vulgaris subspecies was weak. Triturus montandoni haplotypes did not form a monophyletic group. Instead they were found in six clades, in five of them mixed with T. vulgaris haplotypes, most likely as a result of past or ongoing hybridization and multiple introgression of mtDNA from T. vulgaris to T. montandoni. Patterns of sequence variation within clades suggested long-term demographic stability in the southern groups, moderate and relatively old demographic growth in the populations inhabiting central Europe, and high growth in some of the groups that colonized northern parts of Europe after the last glacial maximum.
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Affiliation(s)
- W Babik
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland.
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13
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Abstract
The moor frog Rana arvalis is a lowland species with a broad Eurasiatic distribution, from arctic tundra through forest to the steppe zone. Its present-day range suggests that glacial refugia of this frog were located outside southern European peninsulas. We studied the species-wide phylogeographical pattern using sequence variation in a 682 base pairs fragment of mtDNA cytochrome b gene; 223 individuals from 73 localities were analysed. Two main clades, A and B, differing by c. 3.6% sequence divergence were detected. The A clade is further subdivided into two subclades, AI and AII differing by 1.0%. All three lineages are present in the Carpathian Basin (CB), whereas the rest of the species range, including huge expanses of Eurasian lowlands, are inhabited solely by the AI lineage. We infer that AII and B lineages survived several glacial cycles in the CB but did not expand, at least in the present interglacial, to the north. The geographical distribution and genealogical relationships between haplotypes from the AI lineage indicate that this group had two glacial refugia, one located in the eastern part of the CB and the other probably in southern Russia. Populations from both refugia contributed to the colonization of the western part of the range, whereas the eastern part was colonized from the eastern refugium only. The effective population size as evidenced by theta(ML) is an order of magnitude higher in the AI lineage than in the AII and B lineages. Demographic expansion was detected in all three lineages.
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Affiliation(s)
- W Babik
- Institute of Zoology, Jagiellonian University, Ingardena 6, 30-060 Kraków, Poland.
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14
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Abstract
Frequency data of short tandem repeats (STR) loci included in the AmpF/STR Profiler Plus kit were collected from a sample of 253 random, unrelated individuals born in the south Poland region. All loci met Hardy-Weinberg expectation.
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Affiliation(s)
- P Wolañska-Nowak
- Institute of Forensic Research in Cracow, Forensic Haemogenetics Section, Westerplatte St. 9, 31-33 Cracow, Poland.
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15
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Abstract
Short tandem repeats (STR) are presently of particular use in the field of forensic science, evolution and anthropology. Y-chromosomal STR systems are widely used for population genetics, population history, and for male identification in forensic cases. Here we present an examination of DYS19, DYS390 and DYS393 allele frequencies in a northern Polish population sample. The calculated indices reflect the potential of these markers for application in forensic casework. Statistically significant differences were observed between most western European populations and the Polish cohort when comparing homogeneity of distribution of DYS19 and DYS390 alleles. For three analyzed loci in a sample of 176 males, 43 haplotypes were observed. The studies revealed some rare alleles and a new allele, allele 16, in the DYS393 system. Sequencing by capillary electrophoresis (PE ABI 310) showed the presence of 16 GATA repetitive elements, confirming results obtained after capillary electrophoresis of the DNA fragment. Additionally, sequencing revealed the presence of a novel transversion (A->C) in the analyzed sample.
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Affiliation(s)
- R Pawlowski
- Institute of Forensic Research, Cracow, Poland
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16
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Rokita H, Branicki W, Wrońska D, Borysiewicz LK, Koj A. Vaccinia virus-induced changes in cytokine-regulated acute phase plasma protein synthesis by hepatoma cells. Biochem Mol Biol Int 1998; 44:1093-104. [PMID: 9623762 DOI: 10.1080/15216549800202162] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Human hepatoma cell line, HepG2, has been infected with vaccinia virus and synthesis of plasma proteins was determined by electroimmunoassay and corresponding mRNA's measured by Northern blotting. The inhibitory effect of the virus was dose- and time-dependent. Electrophoretic mobility shift assay revealed a decrease in C/EBP binding activities in nuclear extracts isolated from the infected hepatoma cells. Supershift analysis of the C/EBP isoforms showed alpha and beta subunit involvement in DNA binding. The treatment of the cells with interleukin-1, interleukin-6, and dexamethasone at the initial stage of infection appears to delay the virally induced inhibition of host cell protein synthesis. Thus, possible "protective" role of the acute phase cytokines in viral infection is proposed.
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Affiliation(s)
- H Rokita
- Institute of Molecular Biology, Jagiellonian University, Kraków, Poland.
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