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  • 1.
    Ballantyne, Kaye N.
    et al.
    Erasmus MC University, Netherlands Victoria Police Forens Serv Department, Australia .
    Ralf, Arwin
    Erasmus MC University, Netherlands .
    Aboukhalid, Rachid
    Mohammed V Agdal University, Morocco .
    Achakzai, Niaz M.
    University of Punjab, Pakistan .
    Anjos, Maria J.
    National Institute Legal Medical and Forens Science IP, Portugal .
    Ayub, Qasim
    Wellcome Trust Sanger Institute, England .
    Balazic, Joze
    University of Ljubljana, Slovenia .
    Ballantyne, Jack
    University of Central Florida, FL 32816 USA University of Central Florida, FL 32816 USA .
    J. Ballard, David
    Kings Coll London, England .
    Berger, Burkhard
    Medical University of Innsbruck, Austria .
    Bobillo, Cecilia
    University of Buenos Aires, Argentina Consejo Nacl Invest Cient and Tecn, Argentina .
    Bouabdellah, Mehdi
    Mohammed V Agdal University, Morocco .
    Burri, Helen
    University of Zurich, Switzerland .
    Capal, Tomas
    Institute Criminalist Prague, Czech Republic .
    Caratti, Stefano
    University of Turin, Italy .
    Cardenas, Jorge
    University of Santiago de Compostela, Spain .
    Cartault, Francois
    Site Centre Hospital Felix Guyon, Reunion .
    F. Carvalho, Elizeu
    University of Estado Rio De Janeiro, Brazil .
    Carvalho, Monica
    National Institute Legal Medical and Forens Science IP, Portugal .
    Cheng, Baowen
    Yunnan Prov Department Public Secur, Peoples R China .
    D. Coble, Michael
    NIST, MD 20899 USA .
    Comas, David
    University of Pompeu Fabra, Spain .
    Corach, Daniel
    University of Buenos Aires, Argentina Consejo Nacl Invest Cient and Tecn, Argentina .
    E. DAmato, Maria
    University of Western Cape, South Africa .
    Davison, Sean
    University of Western Cape, South Africa .
    de Knijff, Peter
    Leiden University, Netherlands .
    Corazon A. De Ungria, Maria
    University of Philippines, Philippines .
    Decorte, Ronny
    Katholieke University of Leuven, Belgium .
    Dobosz, Tadeusz
    Wroclaw Medical University, Poland .
    M. Dupuy, Berit
    Norwegian Institute Public Heatlh, Norway .
    Elmrghni, Samir
    University of Benghazi, Libya .
    Gliwinski, Mateusz
    Medical University of Gdansk, Poland .
    C. Gomes, Sara
    University of Madeira, Portugal .
    Grol, Laurens
    Netherlands Forens Institute, Netherlands .
    Haas, Cordula
    University of Zurich, Switzerland .
    Hanson, Erin
    University of Central Florida, FL 32816 USA .
    Henke, Juergen
    Institute Blutgruppenforsch LGC GmbH, Germany .
    Henke, Lotte
    Institute Blutgruppenforsch LGC GmbH, Germany .
    Herrera-Rodriguez, Fabiola
    Poder Judicial, Costa Rica .
    R. Hill, Carolyn
    NIST, MD 20899 USA .
    Holmlund, Gunilla
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences.
    Honda, Katsuya
    University of Tsukuba, Japan .
    Immel, Uta-Dorothee
    University of Halle Wittenberg, Germany .
    Inokuchi, Shota
    National Research Institute Police Science, Japan .
    A. Jobling, Mark
    University of Leicester, England .
    Kaddura, Mahmoud
    University of Benghazi, Libya .
    S. Kim, Jong
    Supreme Prosecutors Off, South Korea .
    H. Kim, Soon
    National Forens Serv, South Korea .
    Kim, Wook
    Dankook University, South Korea .
    E. King, Turi
    University of Leicester, England .
    Klausriegler, Eva
    Salzburg University, Austria .
    Kling, Daniel
    Norwegian Institute Public Heatlh, Norway .
    Kovacevic, Lejla
    Institute Genet Engn and Biotechnol, Bosnia and Herceg .
    Kovatsi, Leda
    Aristotle University of Thessaloniki, Greece .
    Krajewski, Pawel
    Medical University of Warsaw, Poland .
    Kravchenko, Sergey
    NASU, Ukraine .
    H. D. Larmuseau, Maarten
    Katholieke University of Leuven, Belgium .
    Young Lee, Eun
    Yonsei University, South Korea .
    Lessig, Ruediger
    University of Halle Wittenberg, Germany .
    A. Livshits, Ludmila
    NASU, Ukraine .
    Marjanovic, Damir
    Institute Genet Engn and Biotechnol, Bosnia and Herceg .
    Minarik, Marek
    Genomac Forens Institute, Czech Republic .
    Mizuno, Natsuko
    National Research Institute Police Science, Japan .
    Moreira, Helena
    University of Aveiro, Portugal .
    Morling, Niels
    University of Copenhagen, Denmark .
    Mukherjee, Meeta
    Govt India, India .
    Munier, Patrick
    Site Centre Hospital Felix Guyon, Reunion .
    Nagaraju, Javaregowda
    Centre DNA Fingerprinting and Diagnost, India .
    Neuhuber, Franz
    Salzburg University, Austria .
    Nie, Shengjie
    Kunming Medical University, Peoples R China .
    Nilasitsataporn, Premlaphat
    Royal Thai Police, Thailand .
    Nishi, Takeki
    University of Tsukuba, Japan .
    H. Oh, Hye
    Supreme Prosecutors Off, South Korea .
    Olofsson, Jill
    University of Copenhagen, Denmark .
    Onofri, Valerio
    University of Politecn Marche, Italy .
    U. Palo, Jukka
    University of Helsinki, Finland .
    Pamjav, Horolma
    Minist Public Adm and Justice, Hungary .
    Parson, Walther
    Medical University of Innsbruck, Austria Penn State University, PA 16802 USA .
    Petlach, Michal
    Genomac Forens Institute, Czech Republic .
    Phillips, Christopher
    University of Santiago de Compostela, Spain .
    Ploski, Rafal
    Medical University of Warsaw, Poland .
    P. R. Prasad, Samayamantri
    Centre DNA Fingerprinting and Diagnost, India .
    Primorac, Dragan
    Penn State University, PA 16802 USA University of New Haven, CT USA University of Split, Croatia University of Osijek, Croatia .
    A. Purnomo, Gludhug
    Eijkman Institute Molecular Biol, Indonesia .
    Purps, Josephine
    Charite, Germany .
    Rangel-Villalobos, Hector
    University of Guadalajara CUCienega UdeG, Mexico .
    Rebala, Krzysztof
    Medical University of Gdansk, Poland .
    Rerkamnuaychoke, Budsaba
    Mahidol University, Thailand .
    Rey Gonzalez, Danel
    University of Santiago de Compostela, Spain .
    Robino, Carlo
    University of Turin, Italy .
    Roewer, Lutz
    Charite, Germany .
    Rosa, Alexandra
    University of Madeira, Portugal University of Madeira, Portugal .
    Sajantila, Antti
    University of Helsinki, Finland University of N Texas, TX USA .
    Sala, Andrea
    University of Buenos Aires, Argentina Consejo Nacl Invest Cient and Tecn, Argentina .
    M. Salvador, Jazelyn
    University of Philippines, Philippines .
    Sanz, Paula
    University of Pompeu Fabra, Spain .
    Schmitt, Cornelia
    University of Cologne, Germany .
    K. Sharma, Anil
    Govt India, India .
    A. Silva, Dayse
    University of Estado Rio De Janeiro, Brazil .
    Shin, Kyoung-Jin
    Yonsei University, South Korea .
    Sijen, Titia
    Netherlands Forens Institute, Netherlands .
    Sirker, Miriam
    University of Cologne, Germany .
    Sivakova, Daniela
    Comenius University, Slovakia .
    Skaro, Vedrana
    Genos Ltd, Croatia .
    Solano-Matamoros, Carlos
    University of Costa Rica, Costa Rica .
    Souto, Luis
    University of Aveiro, Portugal .
    Stenzl, Vlastimil
    Institute Criminalist Prague, Czech Republic .
    Sudoyo, Herawati
    Eijkman Institute Molecular Biol, Indonesia .
    Syndercombe-Court, Denise
    Kings Coll London, England .
    Tagliabracci, Adriano
    University of Politecn Marche, Italy .
    Taylor, Duncan
    Forens Science South Australia, Australia Flinders University of S Australia, Australia .
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Linkoping, Sweden .
    S. Tsybovsky, Iosif
    State Comm Forens Expertises, Byelarus .
    Tyler-Smith, Chris
    Wellcome Trust Sanger Institute, England .
    J. van der Gaag, Kristiaan
    Leiden University, Netherlands .
    Vanek, Daniel
    Forens DNA Serv, Czech Republic Charles University of Prague, Czech Republic .
    Volgyi, Antonia
    Minist Public Adm and Justice, Hungary .
    Ward, Denise
    Forens Science South Australia, Australia .
    Willemse, Patricia
    Leiden University, Netherlands .
    P. H. Yap, Eric
    DSO National Labs, Singapore .
    Y. Y. Yong, Rita
    DSO National Labs, Singapore .
    Zupanic Pajnic, Irena
    University of Ljubljana, Slovenia .
    Kayser, Manfred
    Erasmus MC University, Netherlands .
    Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats2014In: Human Mutation, ISSN 1059-7794, E-ISSN 1098-1004, Vol. 35, no 8, p. 1021-1032Article in journal (Refereed)
    Abstract [en]

    Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, greater than99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father-son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RMY-STRs in identifying and separating unrelated and related males and provides a reference database.

  • 2.
    Dorum, Guro
    et al.
    Norwegian University of Life Science, Norway.
    Kling, Daniel
    Norwegian University of Life Science, Norway; Norwegian Institute Public Heatlh, Norway.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Dehli Vigeland, Magnus
    University of Oslo, Norway; Oslo University Hospital, Norway.
    Egeland, Thore
    Norwegian University of Life Science, Norway.
    Mixtures with relatives and linked markers2016In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 130, no 3, p. 621-634Article in journal (Refereed)
    Abstract [en]

    Mixture DNA profiles commonly appear in forensic genetics, and a large number of statistical methods and software are available for such cases. However, most of the literature concerns mixtures where the contributors are assumed unrelated and the genetic markers are unlinked. In this paper, we consider mixtures of linked markers and related contributors. If no relationships are involved, linkage can be ignored. While unlinked markers can be treated independently, linkage introduces dependencies. The use of linked markers presents statistical and computational challenges, but may also lead to a considerable increase in power since the number of markers available is much larger if we do not require the markers to be unlinked. In addition, some cases that cannot be solved with an unlimited number of unlinked autosomal markers can be solved with linked markers. We focus on two special cases of linked markers: pairs of linked autosomal markers and X-chromosomal markers. A framework is presented for calculation of likelihood ratios for mixtures with general relationships and with linkage between any number of markers. Finally, we explore the effect of linkage disequilibrium, also called allelic association, on the likelihood ratio.

  • 3.
    Grandell, Ida
    et al.
    National Board Forens Med, Department Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    Samara, Raed
    QIAGEN Science Inc, MD 21703 USA.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    A SNP panel for identity and kinship testing using massive parallel sequencing2016In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 130, no 4, p. 905-914Article in journal (Refereed)
    Abstract [en]

    Within forensic genetics, there is still a need for supplementary DNA marker typing in order to increase the power to solve cases for both identity testing and complex kinship issues. One major disadvantage with current capillary electrophoresis (CE) methods is the limitation in DNA marker multiplex capability. By utilizing massive parallel sequencing (MPS) technology, this capability can, however, be increased. We have designed a customized GeneRead DNASeq SNP panel (Qiagen) of 140 previously published autosomal forensically relevant identity SNPs for analysis using MPS. One single amplification step was followed by library preparation using the GeneRead Library Prep workflow (Qiagen). The sequencing was performed on a MiSeq System (Illumina), and the bioinformatic analyses were done using the software Biomedical Genomics Workbench (CLC Bio, Qiagen). Forty-nine individuals from a Swedish population were genotyped in order to establish genotype frequencies and to evaluate the performance of the assay. The analyses showed to have a balanced coverage among the included loci, and the heterozygous balance showed to have less than 0.5 % outliers. Analyses of dilution series of the 2800M Control DNA gave reproducible results down to 0.2 ng DNA input. In addition, typing of FTA samples and bone samples was performed with promising results. Further studies and optimizations are, however, required for a more detailed evaluation of the performance of degraded and PCR-inhibited forensic samples. In summary, the assay offers a straightforward sample-to-genotype workflow and could be useful to gain information in forensic casework, for both identity testing and in order to solve complex kinship issues.

  • 4.
    Green, Henrik
    et al.
    Linköping University, Department of Medical and Health Sciences, Division of Drug Research. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Hematopoiesis and Developmental Biology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Pettersson, Gisela
    Natl Board Forens Med, Sweden.
    Montelius, Kerstin
    Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, S-58758 Linkoping, Sweden.
    The use of FTA cards to acquire DNA profiles from postmortem cases2019In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 133, no 6, p. 1651-1657Article in journal (Refereed)
    Abstract [en]

    Filter papers have been used for many years in different applications of molecular biology and have been proven to be a stable way to store DNA waiting to be analyzed. Sampling of DNA on FTA (Flinders Technology Associates) cards is convenient and cost effective compared to alternative approaches involving DNA extractions and storage of DNA extracts. FTA cards are analyzed at many forensic laboratories, and the way to perform direct genetic profiling on buccal swab cards has developed into an almost industrial process. The possibility to include postmortem (PM) samples into an FTA-based workflow would facilitate and speed up the genetic identification process compared to conventional methods, both on a regular basis and in a mass casualty event. In this study, we investigated if FTA cards may be used to carry tissue DNA from deceased and present a high-quality DNA profile from the individual in order to be useful for the identification process. The study also aimed to investigate if a specific body tissue would be preferable, and if decomposed tissue is suitable at all to put on an FTA card in order to obtain a DNA profile. We have compared the quality of the DNA profiles acquired from postmortem tissue on FTA cards, with the results acquired with conventional methods from reference bone/muscle samples from the same individual. Several types of tissues have been tested from different identification cases and scenarios. We concluded that tissue cells from inner organs are suitable to put on FTA cards, and that the obtained DNA profiles have the potential to serve as PM data for identification purposes. In cases including compromised samples, however, it is recommended to keep the tissue sample as a backup if further DNA has to be extracted.

  • 5.
    Kling, Daniel
    et al.
    Norwegian Institute Public Heatlh, Norway; Norwegian University of Life Science, Norway.
    DellAmico, Barbara
    National Board Forens Med, Department Forens Genet and Forens Toxicol, SE-58758 Linkoping, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, SE-58758 Linkoping, Sweden.
    FamLinkX - implementation of a general model for likelihood computations for X-chromosomal marker data2015In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 17Article in journal (Refereed)
    Abstract [en]

    The use of genetic markers located on the X chromosome has seen a significant increase in the last years and their utility has been well studied. This paper describes the software FamLinkX, freely available at http://www.famlink.se, implementing a new algorithm for likelihood computations accounting for linkage, linkage disequilibrium and mutations. It is obvious that such software is sought for among forensic users as more and more X-chromosomal markers become available. We provide some simulated examples demonstrating the utility of the implementation as well as its application in forensic casework. Though algebraic derivations are generally unfeasible, the paper outlines some theoretical considerations and provides a discussion on the validation of the software. The focus of this paper is to compare the software to existing methods in a forensic setting, perform a validation study as well as to provide an idea of the discriminatory power for X-chromosomal markers. (C) 2015 Elsevier Ireland Ltd. All rights reserved.

  • 6.
    Kling, Daniel
    et al.
    Oslo Univ Hosp, Norway.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Hematopoiesis and Developmental Biology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Forensic genealogy-A comparison of methods to infer distant relationships based on dense SNP data2019In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 42, p. 113-124Article in journal (Refereed)
    Abstract [en]

    The concept forensic genealogy was discussed already in 2005 but has recently emerged in relation to the use of public genealogy databases to find relatives of the donor of a crime stain. In this study we explored the results and evaluation of searches conducted in such databases. In particular, we focused on the statistical classification that entails from the search and study the variation observed for different relationship classes. The forensic guidelines advocate the use of the likelihood ratio (LR) as a mean to measure the weight of evidence, which requires exact formulation of competing hypotheses. We contrast the LR approach with alternative approaches relying on identical by state (IBS) measures to estimate the total length of shared genomic segments as well as identical by descent (IBD) coefficients for a pair of individuals. We used freely accessible data from the 1000 Genome project to perform extensive simulations, generating data for a number of distinct relationships. Specifically we studied some overarching relationship classes and the performance of the above-mentioned evaluative approaches to classify a known pair of relatives into each class. The results indicate that the traditional LR approach as a single source of classification is as good as, and in some cases even better than, the alternative approaches. In particular the true classification rate is higher for some distant relationship. However, the LR approach is both computer-intensive and sensitive to population frequencies as well as genetic maps (positions of the markers). We further showed that when combining different classification approaches, a lower false classification rate was achieved while still maintaining a high true classification rate.

  • 7.
    Kling, Daniel
    et al.
    Department of Forensic Services, Oslo University Hospital, Oslo, Norway.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
    Kinship inference for males with identical Y-STR profiles using whole genome SNP data provides a deeper understanding about the level of coancestry in the Swedish male population2017In: Forensic Science International: Genetics Supplement Series, ISSN 1875-1768, E-ISSN 1875-175X, Vol. 6, p. e393-e394Article in journal (Refereed)
    Abstract [en]

    Male individuals, from a Swedish reference population, with identical 17 loci Y-chromosomal STR haplotypes were analyzed with more than 900,000 autosomal SNPs in order to estimate their degree of genetic relatedness. This study shows that even though identical Y-STR profiles are shared, there is no evidence that these individuals are related to a higher degree compared with randomly unrelated male individuals in the Swedish population. Based on the results in this study, we conclude that the data do not show any signs of a biased sampling when it comes to the studied male individuals representing the Swedish reference population. © 2017 Elsevier B.V.

  • 8.
    Kling, Daniel
    et al.
    Norwegian Institute Public Heatlh, Norway; Norwegian University of Life Science, Norway.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Egeland, Thore
    Norwegian University of Life Science, Norway; Norwegian Institute Public Heatlh, Norway.
    Mostad, Petter
    Norwegian University of Life Science, Norway; University of Gothenburg, Sweden.
    A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations2015In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 129, no 5, p. 943-954Article in journal (Refereed)
    Abstract [en]

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  • 9.
    Kling, Daniel
    et al.
    Norwegian Institute Public Heatlh, Norway; Norwegian University of Life Science, Norway.
    Tillmar, Andreas O.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Egeland, Thore
    Norwegian University of Life Science, Norway; Norwegian Institute Public Heatlh, Norway.
    Familias 3-Extensions and new functionality2014In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 13, p. 121-127Article in journal (Refereed)
    Abstract [en]

    In relationship testing the aim is to determine the most probable pedigree structure given genetic marker data for a set of persons. Disaster Victim Identification (DVI) based on DNA data from presumed relatives of the missing persons can be considered to be a collection of relationship problems. Forensic calculations in investigative mode address questions like "How many markers and reference persons are needed? Such questions can be answered by simulations. Mutations, deviations from Hardy-Weinberg Equilibrium (or more generally, accounting for population substructure) and silent alleles cannot be ignored when evaluating forensic evidence in case work. With the advent of new markers, so called microvariants have become more common. Previous mutation models are no longer appropriate and a new model is proposed. This paper describes methods designed to deal with DVI problems and a new simulation model to study distribution of likelihoods. There are softwares available, addressing similar problems. However, for some problems including DVI, we are not aware of freely available validated software. The Familias software has long been widely used by forensic laboratories worldwide to compute likelihoods in relationship scenarios, though previous versions have lacked desired functionality, such as the above mentioned. The extensions as well as some other novel features have been implemented in the new version, freely available at www.familias.no. The implementation and validation are briefly mentioned leaving complete details to Supplementary sections.

  • 10.
    Sidstedt, M.
    et al.
    Swedish National Forensic Centre, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden.
    Grandell, I.
    Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
    Boiso, S.
    Swedish National Forensic Centre, Linköping, Sweden.
    Sanga, Malin
    Swedish National Forensic Centre, Linköping, Sweden.
    Gréen, Henrik
    Linköping University, Department of Medical and Health Sciences, Division of Drug Research. Linköping University, Faculty of Medicine and Health Sciences. Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
    Hedman, J.
    Swedish National Forensic Centre, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
    Assessing the GeneRead SNP panel for analysis of low-template and PCR-inhibitory samples2017In: Forensic Science International: Genetics Supplement Series, ISSN 1875-1768, E-ISSN 1875-175X, Vol. 6, p. e267-e269Article in journal (Refereed)
    Abstract [en]

    Massive parallel sequencing (MPS) is increasingly used for human identification purposes in forensic DNA laboratories. Forensic DNA samples are by nature heterogeneous and of varying quality, both concerning DNA integrity and matrices, creating a need for assays that can handle low amounts of DNA as well as impurities. Commercial short tandem repeat (STR) analysis kits for capillary electrophoresis-based separation have evolved drastically over the past years to handle low-template samples and high amounts of various PCR inhibitors. If MPS is to be used extensively in forensic laboratories there is a need to ascertain a similar performance. We have evaluated the GeneRead Individual Identity SNP panel (Qiagen) that includes 140 SNP markers, following the GeneRead DNAseq Targeted Panels V2 handbook for library preparation, applying low levels of DNA and relevant impurities. Analysis of down to 0.1 ng DNA generated SNP profiles with at least 85% called SNPs, after increasing the number of PCR cycles in the initial PCR from 20 to 24. The SNP assay handled extracts from four different DNA extraction methods, including Chelex with blood and saliva, without detrimental effects. Further, the assay was shown to tolerate relevant amounts of inhibitor solutions from soil, cigarettes, snuff and chewing gum. In conclusion, the performance of the SNP panel was satisfactory for casework-like samples. © 2017 Elsevier B.V.

  • 11.
    Staadig, A.
    et al.
    Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    An overall limited effect on the weight-of-evidence when taking STR DNA sequence polymorphism into account in kinship analysis2019In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 39, p. 44-49Article in journal (Refereed)
    Abstract [en]

    The recent years development of massively parallel sequencing (MPS) instruments and assays have now made it a compatible complement to the established capillary electrophoresis (CE) analysis for different forensic genetic applications. It is well known that short tandem repeat (STR) alleles of the same fragment size could have different DNA sequences. Thus, there will be an expected increase in the population genetic diversity for the present set of forensic STRs when performing the analysis with MPS technologies and taking the internal DNA sequence into account. In order to study the additional value of this increase of information for kinship analysis casework, we set up an allele frequency database for the Swedish population for the autosomal markers included in the ForenSeq (TM) DNA Signature Prep Kit (Illumina). A total of 298 individuals with Swedish origin were analyzed and allele frequency distributions based on DNA sequence polymorphisms for 27 autosomal STRs were established. As expected, the results showed an addition in number of observed alleles with 55% in total compared with fragment length based allele definitions, however, a majority only appeared in a few number of observations. In addition, simulations were performed in order to study the impact of the increase in number of observed alleles for the expected likelihood ratios (LRs) for different kinship case scenarios. Only a minor increase of the LRs were, however, observed when taking allele sequence variations in addition with fragment length variations into account compared to only considering fragment length variations. Further studies are required to see if it is cost effective to implement this technique that, according to this study, only has a limited overall additive effect for kinship testing. Although, in specific cases MPS methods will increase the discrimination power due to that, even if in a low frequency, a high genetic diversity exist and the differentiation could be more significant. The establishment of the allele frequency database will enable biostatistical calculations to be performed in casework.

  • 12.
    Söderberg, Carl
    et al.
    Karolinska Institute, Sweden; National Board Forens Med, Department Forens Med, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Wernvik, Emma
    National Board Forens Med, Department Forens Med, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Chemistry, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Spigset, Olav
    St Olavs University Hospital, Norway; Norwegian University of Science and Technology, Norway.
    Kronstrand, Robert
    Linköping University, Department of Medical and Health Sciences, Division of Drug Research. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Chemistry, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Reis, Margareta
    Linköping University, Department of Medical and Health Sciences, Division of Drug Research. Linköping University, Faculty of Medicine and Health Sciences. Skåne University Hospital, Sweden.
    Jonsson, Anna K.
    National Board Forens Med, Department Forens Genet and Forens Chemistry, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Druid, Henrik
    Karolinska Institute, Sweden; National Board Forens Med, Department Forens Med, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Antipsychotics - Postmortem fatal and non-fatal reference concentrations2016In: Forensic Science International, ISSN 0379-0738, E-ISSN 1872-6283, Vol. 266, p. 91-101Article in journal (Refereed)
    Abstract [en]

    Making the diagnosis fatal intoxication is a challenging task for the forensic pathologist and toxicologist, particularly when the cases involve substances where reference information is scarce or not at all available. This study presents postmortem femoral blood concentrations for 24 antipsychotic substances, based on samples collected and analyzed from 4949 autopsy cases in Sweden during 1992-2010. In addition our study provides information about the prevalence of different antipsychotics in accidental, suicidal, homicidal and uncertain deaths. The data have been selected and evaluated according to strict inclusion and exclusion criteria as well as a manual, multi-reviewer, case-by-case evaluation. The reference information is subdivided into intoxications by one specific substance only (group A, n = 259), multi-substance intoxications (group B, n = 614) and postmortem controls, consisting of deaths not involving incapacitation by substances (group C, n = 507). Moreover, the results are compared with data based on therapeutic drug monitoring, and data collected from driving under the influence cases. Median concentrations in group A were significantly higher than in group C for all substances evaluated. For 17 of 24 substances, the median concentrations in group B were significantly higher than in group C. In general, the therapeutic drug monitoring and driving under the influence concentrations were similar to, or lower than, the concentrations in group C. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

  • 13.
    Tillmar, Andreas
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    Kling, Daniel
    Norwegian Institute Public Heatlh, Norway.
    Letter: Comments on "Kinship analysis: assessment of related vs unrelated based on defined pedigrees" by S. Turrina et al. in INTERNATIONAL JOURNAL OF LEGAL MEDICINE, vol 130, issue 4, pp 949-9512016In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 130, no 4, p. 949-951Article in journal (Other academic)
    Abstract [en]

    n/a

  • 14.
    Tillmar, Andreas
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    Kling, Daniel
    Oslo University Hospital, Norway.
    Butler, John M.
    NIST, MD 20899 USA.
    Parson, Walther
    Medical University of Innsbruck, Austria; Penn State University, PA 16802 USA.
    Prinz, Mechthild
    John Jay Coll Criminal Justice, NY USA.
    Schneider, Peter M.
    University of Cologne, Germany.
    Egeland, Thore
    Norwegian University of Life Science, Norway.
    Gusmao, Leonor
    State University of Rio de Janeiro UERJ, Brazil.
    DNA Commission of the International Society for Forensic Genetics ( ISFG): Guidelines on the use of X-STRs in kinship analysis2017In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 29, p. 269-275Article in journal (Refereed)
    Abstract [en]

    Forensic genetic laboratories perform an increasing amount of genetic analyses of the X chromosome, in particular to solve complex cases of kinship analysis. For some biological relationships X-chromosomal markers can be more informative than autosomal markers, and there are a large number of markers, methods and databases that have been described for forensic use. Due to their particular mode of inheritance, and their physical location on a single chromosome, some specific considerations are required when estimating the weight of evidence for X-chromosomal marker DNA data. The DNA Commission of the International Society for Forensic Genetics (ISFG) hereby presents guidelines and recommendations for the use of X-chromosomal markers in kinship analysis with a special focus on the biostatistical evaluation. Linkage and linkage disequilibrium (association of alleles) are of special importance for such evaluations and these concepts and the implications for likelihood calculations are described in more detail. Furthermore it is important to use appropriate computer software that accounts for linkage and linkage disequilibrium among loci, as well as for mutations. Even though some software exist, there is still a need for further improvement of dedicated software. (C) 2017 Elsevier B.V. All rights reserved.

  • 15.
    Tillmar, Andreas O.
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Mostad, Petter
    University of Gothenburg, Sweden; Norwegian University of Life Science, Norway.
    Choosing supplementary markers in forensic casework2014In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 13, p. 128-133Article in journal (Refereed)
    Abstract [en]

    The vast majority of human familial identifications based on DNA end up with a well founded conclusion, normally using a standard set of genetic short tandem repeat (STR) loci. There are, however, a proportion of cases that show ambiguous results. For such occasions a number of different supplementary markers could be typed in order to gain further information. There are numerous markers available for such supplementary DNA typing, including STRs, deletion and insertion polymorphisms (DIPs), and single nucleotide polymorphisms (SNPs). The purpose of this work was to describe a precise method for decision making, aiming to aid the comparison of different sets of markers for different case scenarios in order to find the most efficient set for routine casework. Comparisons are based on a particular function relating the expected additional value of information from new data to the amount of information already obtained from initial data. The function can be computed approximately by approximating likelihood-based error rates using simulation. In this paper we focused on paternity investigations, more specifically the use of supplementary markers in cases where a smaller number of genetic inconsistencies make the matter inconclusive. We applied the method to a comparison of three different kits: Investigator HDplex (STRs), Investigator DIPplex (DIPs), and the SNPforID-plex (SNPs) to study their efficiencies in gaining information in different case scenarios involving various alternative relationships between the tested man and the tested child. We show that the Investigator HDplex was the most efficient set of supplementary markers for the standard paternity case. However, for paternity cases with a close relative being the alternative father, the Investigator HDplex and the SNPforID-plex showed similar patterns in their ability to deliver a well-founded conclusion. The Investigator DIPplex was the least efficient set.

  • 16.
    Tillmar, Andreas
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences. National Board Forens Med, Department Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    Phillips, Chris
    University of Santiago Compostela, Spain.
    Evaluation of the impact of genetic linkage in forensic identity and relationship testing for expanded DNA marker sets2017In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 26, p. 58-65Article in journal (Refereed)
    Abstract [en]

    Advances in massively parallel sequencing technology have enabled the combination of a much-expanded number of DNA markers (notably STRs and SNPs in one or combined multiplexes), with the aim of increasing the weight of evidence in forensic casework. However, when data from multiple loci on the same chromosome are used, genetic linkage can affect the final likelihood calculation. In order to study the effect of linkage for different sets of markers we developed the biostatistical tool ILIR, (Impact of Linkage on forensic markers for Identity and Relationship tests). The ILIR tool can be used to study the overall impact of genetic linkage for an arbitrary set of markers used in forensic testing. Application of ILIR can be useful during marker selection and design of new marker panels, as well as being highly relevant for existing marker sets as a way to properly evaluate the effects of linkage on a case-by-case basis. ILIR, implemented via the open source platform R, includes variation and genomic position reference data for over 40 STRs and 140 SNPs, combined with the ability to include additional forensic markers of interest. The use of the software is demonstrated with examples from several different established marker sets (such as the expanded CODIS core loci) including a review of the interpretation of linked genetic data. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

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