| 1. |
- Berglund, Martina, et al.
(författare)
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HELIX Competence Centre – Knowledge for Sustainable Working Life
- 2017
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The purpose of this paper is to describe HELIX Competence Centre at Linköping University and its work to contribute to sustainable working life. Research in HELIX Competence Centre is based on an interactive approach between researchers from different disciplines and partner organizations, including industrial organizations, public organizations, labour market organizations, and civil society organizations. The research programme includes four research themes: 1) Sustainable development processes in industrial production systems; 2) Growth and development in small enterprises; 3) Sustainable, innovative, and coordinated health and welfare processes; and 4) Diversity and inclusion in working life. Other activities include seminars and partnership meetings with different topics and a yearly HELIX day. The research and activities led by HELIX Competence Centre constitute an approach to integrate social and economic sustainability, produce scientific knowledge, and add value to practice in the partner organizations.
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| 2. |
- Dorum, Guro, et al.
(författare)
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Mixtures with relatives and linked markers
- 2016
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Ingår i: International journal of legal medicine. - : SPRINGER. - 0937-9827 .- 1437-1596. ; 130:3, s. 621-634
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 3. |
- Elg, Mattias, 1968-, et al.
(författare)
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Sustainable working life development through interactive research
- 2018
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Ingår i: PIN-C Conference Proccedings. ; , s. 1-5
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Interactive research has emerged as a new approach to collaborative research in working life research, and it is characterized by a continuous joint learning process between the researchers and the practitioners. In this paper we argue that interactive research is a way to advance scientific knowledge about the development of new types of work arrangements and development of sustainable working life. We present the basic ideas and benefits of the interactive research approach, illustrated through a practical case, the HELIX Competence Centre and discuss potential limitation and challenges associated with this form of collaborative research.
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| 4. |
- Grandell, Ida, et al.
(författare)
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A SNP panel for identity and kinship testing using massive parallel sequencing
- 2016
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Ingår i: International journal of legal medicine. - : SPRINGER. - 0937-9827 .- 1437-1596. ; 130:4, s. 905-914
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Green, Henrik, et al.
(författare)
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The use of FTA cards to acquire DNA profiles from postmortem cases
- 2019
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Ingår i: International journal of legal medicine. - : SPRINGER. - 0937-9827 .- 1437-1596. ; 133:6, s. 1651-1657
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- Junker, Klara, et al.
(författare)
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Phenotype prediction accuracy – A Swedish perspective
- 2019
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Ingår i: Forensic Science International: Genetics Supplement Series. - : Elsevier BV. - 1875-1768 .- 1875-175X. ; 7:1, s. 384-386
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Tidskriftsartikel (refereegranskat)abstract
- 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 ≥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.
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| 7. |
- Kling, D., et al.
(författare)
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A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations
- 2015
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Ingår i: International Journal of Legal Medicine. - : Springer Science and Business Media LLC. - 0937-9827 .- 1437-1596. ; 129:5, s. 943-954
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
- Kling, Daniel, et al.
(författare)
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FamLinkX - implementation of a general model for likelihood computations for X-chromosomal marker data
- 2015
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 9. |
- Kling, Daniel, et al.
(författare)
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Forensic genealogy-A comparison of methods to infer distant relationships based on dense SNP data
- 2019
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Ingår i: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 42, s. 113-124
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Tidskriftsartikel (refereegranskat)abstract
- 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.
(författare)
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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 population
- 2017
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Ingår i: Forensic Science International. - : Elsevier BV. - 1875-1768 .- 1875-175X. ; 6, s. e393-e394
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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