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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.

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  • 2.
    Bergseth, Erik F.
    et al.
    Oslo Univ Hosp, Norway.
    Tillmar, Andreas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Linkoping, Sweden.
    Haddeland, Jorgen T.
    Oslo Univ Hosp, Norway.
    Kling, Daniel
    Oslo Univ Hosp, Norway; Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Linkoping, Sweden.
    Extended population genetic analysis of 12 X-STRs - Exemplified using a Norwegian population sample2022In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 60, article id 102745Article in journal (Refereed)
    Abstract [en]

    The use of X-chromosomal markers to resolve questions of relatedness has experienced a significant increase during the last years in forensic genetics. Perhaps primarily due to the emergence of commercial kits, but equally important due to an increased awareness of the utility of those markers. The X-chromosomal inheritance pattern entails that some cases, for instance paternal half-sisters, can potentially be resolved using a few X-chromosomal markers alone. For the statistical assessment in kinship cases it is of importance to have relevant population frequency data. In the present study 631 unrelated males from a Norwegian population sample are analyzed. The resulting haplotypes are compared to previously studied population samples and a deeper analysis of the linkage disequilibrium (LD) structure is conducted. We demonstrate that the power to detect LD will be low when few males, say below 300, are analyzed. We use entropy to describe the degree of LD between multiallelic loci and describe how this measure varies between different studied populations. Large population frequency databases have been recommended when using X-chromosomal markers, and we show that by combining reference da-tabases from genetically similar populations, more precise haplotype frequency estimates can be obtained for rare haplotypes which improves the statistical assessment of the weight of evidence. In addition, we promote the use of simulations to assess the utility of STR markers in contrast to standard forensic parameters. Specifically we perform extensive simulations on cases where X-chromosomal markers are important and illustrate how the results can be used to infer the information gained from these markers.

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  • 3.
    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, 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.

  • 4.
    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, 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.

  • 5.
    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, 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.

  • 6.
    Junker, Klara
    et al.
    National Forensic Centre, Sweden.
    Staadig, Adam
    Linköping University, Department of Clinical and Experimental Medicine, Division of Hematopoiesis and Developmental Biology. Linköping University, Faculty of Medicine and Health Sciences. National Board of Forensic Medicine, Sweden.
    Sidstedt, Maja
    National Forensic Centre, Sweden; Lund Univ, 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. National Board of Forensic Medicine, Sweden.
    Hedman, Johannes
    National Forensic Centre, Sweden; Lund Univ, Sweden.
    Phenotype prediction accuracy: A Swedish perspective2019In: Forensic Science International: Genetics Supplement Series, ISSN 1875-1768, E-ISSN 1875-175X, Vol. 7, no 1, p. 384-386Article in journal (Refereed)
    Abstract [en]

    Methods for SNP-based phenotype prediction have recently been developed, but prediction accuracy data for several populations and regions are missing. We analysed the accuracy of hair and eye colour predictions for 111 individuals residing in Sweden, using the ForenSeq system and the MiSeq FGx instrument (Verogen). Observed colours were compared to predicted colours, using the colour with the highest probability value for each prediction. Overall, 80% of eye colour predictions were correct, but the system failed to predict intermediate/green eye colour in our cohort. For hair colour, 58% of predictions were correct, and the majority of incorrect predictions were related to brown hair. To assess if prediction accuracy could be improved by the exclusion of predictions with low probabilities, we applied a threshold of amp;gt;= 0.7. The threshold improved eye colour prediction, from 80% to 85% correct predictions, whereas hair colour prediction accuracy was virtually unaffected (58% versus 57% correct predictions). In summary, the phenotype prediction accuracy was acceptable in our cohort and the use of a threshold was only useful for eye colour predictions.

  • 7.
    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.

  • 8.
    Kling, Daniel
    et al.
    Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Linkoping, Sweden; Oslo Univ Hosp, Norway.
    Phillips, Christopher
    Univ Santiago de Compostela, Spain.
    Kennett, Debbie
    UCL, England.
    Tillmar, Andreas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Linkoping, Sweden.
    Investigative genetic genealogy: Current methods, knowledge and practice2021In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 52, article id 102474Article, review/survey (Refereed)
    Abstract [en]

    Investigative genetic genealogy (IGG) has emerged as a new, rapidly growing field of forensic science. We describe the process whereby dense SNP data, commonly comprising more than half a million markers, are employed to infer distant relationships. By distant we refer to degrees of relatedness exceeding that of first cousins. We review how methods of relationship matching and SNP analysis on an enlarged scale are used in a forensic setting to identify a suspect in a criminal investigation or a missing person. There is currently a strong need in forensic genetics not only to understand the underlying models to infer relatedness but also to fully explore the DNA technologies and data used in IGG. This review brings together many of the topics and examines their effectiveness and operational limits, while suggesting future directions for their forensic validation. We further investigated the methods used by the major direct-to-consumer (DTC) genetic ancestry testing companies as well as submitting a questionnaire where providers of forensic genetic genealogy summarized their operation/ services. Although most of the DTC market, and genetic genealogy in general, has undisclosed, proprietary algorithms we review the current knowledge where information has been discussed and published more openly.

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  • 9.
    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.

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  • 10.
    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.

  • 11.
    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, 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.

  • 12.
    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.

  • 13.
    Loreille, Odile
    et al.
    Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, USA.
    Tillmar, Andreas
    Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Sweden.
    Brandhagen, Michael D.
    Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, USA.
    Otterstatter, Linda
    Federal Bureau of Investigation Laboratory, Trace Evidence Unit, Quantico, USA.
    Irwin, Jodi A.
    Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, USA.
    Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family.2022In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 13, no 2, article id 202Article in journal (Refereed)
    Abstract [en]

    This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina's lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the locket were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas' maternal lineage, including the well-known point heteroplasmy at position 16169.

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  • 14.
    Mostad, Petter
    et al.
    Univ Gothenburg, Sweden; Univ Gothenburg, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Toxicol, Linkoping, Sweden.
    Kling, Daniel
    Natl Board Forens Med, Dept Forens Genet & Toxicol, Linkoping, Sweden; Oslo Univ Hosp, Norway; Norwegian Univ Life Sci, Norway.
    Improved computations for relationship inference using low-coverage sequencing data2023In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 24, no 1, article id 90Article in journal (Refereed)
    Abstract [en]

    Pedigree inference, for example determining whether two persons are second cousins or unrelated, can be done by comparing their genotypes at a selection of genetic markers. When the data for one or more of the persons is from low-coverage next generation sequencing (lcNGS), currently available computational methods either ignore genetic linkage or do not take advantage of the probabilistic nature of lcNGS data, relying instead on first estimating the genotype. We provide a method and software (see familias.name/lcNGS) bridging the above gap. Simulations indicate how our results are considerably more accurate compared to some previously available alternatives. Our method, utilizing a version of the Lander-Green algorithm, uses a group of symmetries to speed up calculations. This group may be of further interest in other calculations involving linked loci.

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  • 15.
    Phillips, C.
    et al.
    Univ Santiago de Compostela, Spain.
    Amigo, J.
    IDIS, Spain.
    Tillmar, Andreas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Peck, M. A.
    Int Commiss Missing Persons, Netherlands.
    de la Puente, M.
    Univ Santiago de Compostela, Spain.
    Ruiz-Ramirez, J.
    Univ Santiago de Compostela, Spain.
    Bittner, F.
    Int Commiss Missing Persons, Netherlands.
    Idrizbegovic, S.
    Int Commiss Missing Persons, Netherlands.
    Wang, Y.
    Qiagen, MD 21703 USA.
    Parsons, T. J.
    Int Commiss Missing Persons, Netherlands.
    Lareu, M. V.
    Univ Santiago de Compostela, Spain.
    A compilation of tri-allelic SNPs from 1000 Genomes and use of the most polymorphic loci for a large-scale human identification panel2020In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 46, article id UNSP 102232Article in journal (Refereed)
    Abstract [en]

    In a directed search of 1000 Genomes Phase III variation data, 271,934 tri-allelic single nucleotide polymorphisms (SNPs) were identified amongst the genotypes of 2,504 individuals from 26 populations. The majority of tri-allelic SNPs have three nucleotide substitution-based alleles at the same position, while a much smaller proportion, which we did not compile, have a nucleotide insertion/deletion plus substitution alleles. SNPs with three alleles have higher discrimination power than binary loci but keep the same characteristic of optimum amplification of the fragmented DNA found in highly degraded forensic samples. Although most of the tri-allelic SNPs identified had one or two alleles at low frequencies, often single observations, we present a full compilation of the genome positions, rs-numbers and genotypes of all tri-allelic SNPs detected by the 1000 Genomes project from the more detailed analyses it applied to Phase III sequence data. A total of 8,705 tri-allelic SNPs had overall heterozygosities (averaged across all 1000 Genomes populations) higher than the binary SNP maximum value of 0.5. Of these, 1,637 displayed the highest average heterozygosity values of 0.6-0.666. The most informative tri-allelic SNPs we identified were used to construct a large-scale human identification panel for massively parallel sequencing, designed for the identification of missing persons. The large-scale MPS identification panel comprised: 1,241 autosomal tri-allelic SNPs and 29 X tri-allelic SNPs (plus 46 microhaplotypes adapted for genotyping from reduced length sequences). Allele frequency estimates are detailed for African, European, South Asian and East Asian population groups plus the Peruvian population sampled by 1000 Genomes for the 1,270 tri-allelic SNPs of the final MPS panel. We describe the selection criteria, kinship simulation experiments and genomic analyses used to select the tri-allelic SNP components of the panel. Approximately 5 % of the tri-allelic SNPs selected for the large-scale MPS identification panel gave three-genotype patterns in single individual samples or discordant genotypes for genomic control DNAs. A likely explanation for some of these unreliably genotyped loci is that they map to multiple sites in the genome - high-lighting the need for caution and detailed scrutiny of multiple-allele variant data when designing future forensic SNP panels, as such patterns can arise from common structural variation in the genome, such as segmental duplications.

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  • 16.
    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.

  • 17.
    Soderberg, C.
    et al.
    Karolinska Inst, Sweden; Natl Board Forens Med, Dept Forens Med, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Johansson, A.
    Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Wernvik, E.
    Natl Board Forens Med, Dept Forens Med, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Jonsson, A. K.
    Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, S-58758 Linkoping, Sweden.
    Druid, H.
    Karolinska Inst, Sweden; Natl Board Forens Med, Dept Forens Med, Artillerigatan 12, S-58758 Linkoping, Sweden.
    The importance of sample size with regard to the robustness of postmortem reference values2020In: Forensic Science International, ISSN 0379-0738, E-ISSN 1872-6283, Vol. 311, article id 110292Article in journal (Refereed)
    Abstract [en]

    Evaluating postmortem toxicological results is a challenging task due to multiple factors affecting blood concentrations after death. In order to improve the diagnostic accuracy in cases of suspected fatal intoxication different compilations of postmortem reference drug concentrations are often used. However, it is not clear what constitutes a reliable postmortem reference value. The current study presents reference concentrations for 13 substances from seven substance groups according to a standardized protocol. The reference concentrations were gathered from 3767 autopsy cases and subdivided into intoxications by one substance only (Group A, n= 611), multi-substance intoxications (Group B, n = 1355) and postmortem controls, in which incapacitation by drugs were excluded (Group C, n = 1801). In particular, this study presents statistical information about the precision and conformity change with various sample sizes. Based on the present data >10 detections are usually needed, for the substances examined, to differentiate between intoxication cases and controls. Repeated samplings show that the median of small samples (N= <= 5) has a high variation (normalized interquartile range 138-75%) and that a high number of detections (N = >20) in each group are needed to reduce the variation. (C) 2020 The Author(s). Published by Elsevier B.V.

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  • 18.
    Staadig, A.
    et al.
    Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    Tillmar, Andreas
    Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Division of Hematopoiesis and Developmental Biology. 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.

  • 19.
    Staadig, Adam
    et al.
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, S-58758 Linkoping, Sweden.
    Hedman, Johannes
    Swedish Police Author, Natl Forens Ctr, S-58194 Linkoping, Sweden; Lund Univ, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, S-58758 Linkoping, Sweden.
    Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity2023In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 14, no 4, article id 818Article in journal (Refereed)
    Abstract [en]

    One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often induced during PCR or sequencing. Unique molecular indices (UMIs) are short random nucleotide sequences ligated to each template molecule prior to amplification. Applying UMIs can improve the limit of detection by enabling accurate counting of initial template molecules and removal of erroneous data. In this study, we applied the FORCE panel, which includes similar to 5500 SNPs, with a QIAseq Targeted DNA Custom Panel (Qiagen), including UMIs. Our main objective was to investigate whether UMIs can enhance the sensitivity and accuracy of forensic genotyping and to evaluate the overall assay performance. We analyzed the data both with and without the UMI information, and the results showed that both genotype accuracy and sensitivity were improved when applying UMIs. The results showed very high genotype accuracies (>99%) for both reference DNA and challenging samples, down to 125 pg. To conclude, we show successful assay performance for several forensic applications and improvements in forensic genotyping when applying UMIs.

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  • 20.
    Staadig, Adam
    et al.
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Linkoping, Sweden.
    Tillmar, Andreas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Linkoping, Sweden.
    Evaluation of microhaplotypes in forensic kinship analysis from a Swedish population perspective2021In: International journal of legal medicine, ISSN 0937-9827, E-ISSN 1437-1596, Vol. 135, no 4, p. 1151-1160Article in journal (Refereed)
    Abstract [en]

    The development of massively parallel sequencing (MPS) technology has enabled the discovery of several new types of forensic markers where microhaplotypes are one of these promising novel genetic markers. Microhaplotypes are, commonly, less than 300 nucleotides in length and consist of two or more closely linked single-nucleotide polymorphisms (SNPs). In this study, we have examined a custom-made QIAseq Microhaplotype panel (Qiagen), including 45 different microhaplotype loci. DNA libraries were prepared according to the GeneRead DNAseq Targeted Panels V2 library preparation workflow (Qiagen) and sequenced on a MiSeq FGx instrument (Verogen). We evaluated the performance of the panel based on 75 samples of Swedish origin and haplotype frequencies were established. We performed sensitivity studies and could detect haplotypes at input amounts down to 0.8 ng. We also studied mixture samples with two contributors for which haplotypes, for the minor contributor, were detectable down to the level of 1:100. Furthermore, we executed kinship simulations to evaluate the usefulness of this panel in kinship analysis. The results showed that both paternity and full sibling cases can clearly be solved. When simulating a half sibling versus unrelated case scenario, there were, however, some overlap of the likelihood ratio distributions potentially resulting in inconclusiveness. To conclude, the results of this initial study are promising for further implementation of this microhaplotype assay into the forensic field, although we noticed some primer design issues that could be optimized, which possibly would increase the power of the assay.

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  • 21.
    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.

  • 22.
    Tillmar, Andreas
    et al.
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, Artillerigatan 12, SE-58758 Linkoping, Sweden.
    Fagerholm, Siri Aili
    Swedish Police Author, Natl Forens Ctr, SE-58194 Linkoping, Sweden.
    Staaf, Jan
    Swedish Police Author, Polisreg Ost, Linkoping, Sweden.
    Sjölund, Peter
    Peter Sjolund AB, Sweden.
    Ansell, Ricky
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Swedish Police Author, Natl Forens Ctr, SE-58194 Linkoping, Sweden.
    Getting the conclusive lead with investigative genetic genealogy: A successful case study of a 16 year old double murder in Sweden2021In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 53, article id 102525Article in journal (Refereed)
    Abstract [en]

    On the morning of October 19, 2004, an eight-year-old boy and a 56-year-old woman were stabbed to death on an open street in the city of Linko center dot ping, Sweden. The perpetrator left his DNA at the crime scene, and after 15 years of various investigation efforts, including more than 9000 interrogations and mass DNA screening of more than 6000 men, there were still no clues about the identity of the unknown murderer. The successful application of investigative genetic genealogy (IGG) in the US raised the interest for this tool within the Swedish Police Authority. After legal consultations it was decided that IGG could be applied in this double murder case as a pilot case study. From extensive DNA analysis, including whole-genome sequencing and genotype imputation, DNA data sets were established and searched within both GEDmatch and FamilyTree DNA genealogy databases. A number of fairly distant relatives were found from which family trees were created. The genealogy work resulted in two candidates, two brothers, one of whom matched the crime scene samples by routine STR profiling. The suspect confessed the murders at the initial police hearing and was later convicted of the murders. In this paper we describe the successful application of an emerging technology. We disclose details of the DNA analyses which, due to the poor quality and low quantity of the DNA, required reiterative sequencing and genotype imputation efforts. The successful application of IGG in this double murder case exemplifies its applicability not only in the US but also in Europe. The pressure is now high on the involved authorities to establish IGG as a tool for cold case criminal investigations and for missing person identifications. There is, however, a continuous need to accommodate legal, social and ethical aspects as well.

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    Appendix A: Supplementary material
  • 23.
    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, ISSN 0937-9827, E-ISSN 1437-1596, Vol. 130, no 4, p. 949-951Article in journal (Other academic)
    Abstract [en]

    n/a

  • 24.
    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.

  • 25.
    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.

  • 26.
    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.

  • 27.
    Tillmar, Andreas
    et al.
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Sjolund, Peter
    Peter Sjolund AB, Sweden.
    Lundqvist, Bo
    Swedish Police Author, Sweden.
    Klippmark, Therese
    Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Algenas, Cajsa
    Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Green, Henrik
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Drug Research. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet and Forens Toxicol, Linkoping, Sweden.
    Whole-genome sequencing of human remains to enable genealogy DNA database searches - A case report2020In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 46, article id UNSP 102233Article in journal (Refereed)
    Abstract [en]

    Recently a number of high profile crime cases (e.g. the "Golden State Killer") have successfully been solved or given new leads with the use of genome wide DNA data in combination with pairwise matching from individuals present in genealogy DNA databases. Such databases will primarily involve distant relatives which in turn require a large amount of genetic information, in the range of several hundred thousand to millions of SNPs, to be genotyped. While it nowadays is fairly straightforward to obtain such as data from high quality and high quantity DNA, it is still a challenge for degraded DNA of low quantity such in the case of forensic samples. Here we present a successful effort in obtaining genome-wide genotype data from human remains. The goal was to get investigative leads in order to identify the remains of an unknown male ("the Ekeby man") that was found murdered in the south of Sweden in 2003. Whole-genome sequencing was performed on DNA originating from a bone sample. Three replicates of libraries were prepared using ThruPLEX DNA-seq Kit (Takara) which were sequenced on a HiSeq X instrument (Illumina). A mean coverage of 30X was obtained when the sequencing reads were mapped to a human reference genome. Following further bioinformatic processing, allele calling, quality checks and filtering to match the genealogy DNA database SNPs, genotypes for approximately one million SNPs were established. The resulting SNP genotypes were then used to search for relatives in the genealogy DNA database GEDmatch (www.gedmatch.com). A candidate list of relatives was obtained which was further processed using traditional genealogy methods in order to get leads about the identity of the unknown. In summary, this report shows how whole-genome sequencing successfully can be applied on forensic samples to create the SNP genotypes required for searches in genealogy DNA databases for the purpose of generating leads to identify missing or unknown persons, including perpetrators and victims.

  • 28.
    Tillmar, Andreas
    et al.
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, SE-58758 Linkoping, Sweden.
    Sturk-Andreaggi, Kimberly
    Armed Forces Med Examiner Syst Armed Forces DNA I, DE 19902 USA; SNA Int LLC, VA 22314 USA; Uppsala Univ, Sweden.
    Daniels-Higginbotham, Jennifer
    Armed Forces Med Examiner Syst Armed Forces DNA I, DE 19902 USA; SNA Int LLC, VA 22314 USA.
    Thomas, Jacqueline Tyler
    Armed Forces Med Examiner Syst Armed Forces DNA I, DE 19902 USA; SNA Int LLC, VA 22314 USA.
    Marshall, Charla
    Armed Forces Med Examiner Syst Armed Forces DNA I, DE 19902 USA; SNA Int LLC, VA 22314 USA; Penn State Univ, PA 16802 USA.
    The FORCE Panel: An All-in-One SNP Marker Set for Confirming Investigative Genetic Genealogy Leads and for General Forensic Applications2021In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 12, no 12, article id 1968Article in journal (Refereed)
    Abstract [en]

    The FORensic Capture Enrichment (FORCE) panel is an all-in-one SNP panel for forensic applications. This panel of 5422 markers encompasses common, forensically relevant SNPs (identity, ancestry, phenotype, X- and Y-chromosomal SNPs), a novel set of 3931 autosomal SNPs for extended kinship analysis, and no clinically relevant/disease markers. The FORCE panel was developed as a custom hybridization capture assay utilizing ~20,000 baits to target the selected SNPs. Five non-probative, previously identified World War II (WWII) cases were used to assess the kinship panel. Each case included one bone sample and associated family reference DNA samples. Additionally, seven reference quality samples, two 200-year-old bone samples, and four control DNAs were processed for kit performance and concordance assessments. SNP recovery after capture resulted in a mean of ~99% SNPs exceeding 10X coverage for reference and control samples, and 44.4% SNPs for bone samples. The WWII case results showed that the FORCE panel could predict first to fifth degree relationships with strong statistical support (likelihood ratios over 10,000 and posterior probabilities over 99.99%). To conclude, SNPs will be important for further advances in forensic DNA analysis. The FORCE panel shows promising results and demonstrates the utility of a 5000 SNP panel for forensic applications.

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