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Tillmar, Andreas
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Publications (10 of 10) Show all publications
Sidstedt, M., Grandell, I., Boiso, S., Sanga, M., Gréen, H., Hedman, J. & Tillmar, A. (2017). Assessing the GeneRead SNP panel for analysis of low-template and PCR-inhibitory samples. Forensic Science International: Genetics Supplement Series, 6, e267-e269
Open this publication in new window or tab >>Assessing the GeneRead SNP panel for analysis of low-template and PCR-inhibitory samples
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2017 (English)In: Forensic Science International: Genetics Supplement Series, ISSN 1875-1768, E-ISSN 1875-175X, Vol. 6, p. e267-e269Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2017
Keywords
Forensic DNA analysis; Human identification; Massive parallel sequencing; Next generation sequencing; Single nucleotide polymorphism
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:liu:diva-146972 (URN)10.1016/j.fsigss.2017.09.088 (DOI)2-s2.0-85029660404 (Scopus ID)
Available from: 2018-04-09 Created: 2018-04-09 Last updated: 2018-04-09
Kling, D. & Tillmar, A. (2017). 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. Forensic Science International: Genetics Supplement Series, 6, e393-e394
Open this publication in new window or tab >>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 (English)In: Forensic Science International: Genetics Supplement Series, ISSN 1875-1768, E-ISSN 1875-175X, Vol. 6, p. e393-e394Article in journal (Refereed) Published
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.

Keywords
Population genetics; Sweden; Y chromosome
National Category
Analytical Chemistry
Identifiers
urn:nbn:se:liu:diva-146970 (URN)10.1016/j.fsigss.2017.09.165 (DOI)2-s2.0-85030470547 (Scopus ID)
Available from: 2018-04-09 Created: 2018-04-09 Last updated: 2018-04-09
Grandell, I., Samara, R. & Tillmar, A. (2016). A SNP panel for identity and kinship testing using massive parallel sequencing. International journal of legal medicine (Print), 130(4), 905-914
Open this publication in new window or tab >>A SNP panel for identity and kinship testing using massive parallel sequencing
2016 (English)In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 130, no 4, p. 905-914Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
SPRINGER, 2016
Keywords
Next generation sequencing; Single-nucleotide polymorphism; Forensic genetics; Human identification; Kinship
National Category
Forensic Science
Identifiers
urn:nbn:se:liu:diva-130267 (URN)10.1007/s00414-016-1341-4 (DOI)000378817900003 ()26932869 (PubMedID)
Available from: 2016-08-01 Created: 2016-07-28 Last updated: 2017-11-28
Tillmar, A. & Kling, D. (2016). 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 949-951 [Letter to the editor]. International journal of legal medicine (Print), 130(4), 949-951
Open this publication in new window or tab >>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 949-951
2016 (English)In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 130, no 4, p. 949-951Article in journal, Letter (Other academic) Published
Abstract [en]

n/a

Place, publisher, year, edition, pages
SPRINGER, 2016
National Category
Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-130268 (URN)10.1007/s00414-016-1316-5 (DOI)000378817900009 ()26797423 (PubMedID)
Available from: 2016-08-01 Created: 2016-07-28 Last updated: 2017-11-28
Dorum, G., Kling, D., Tillmar, A., Dehli Vigeland, M. & Egeland, T. (2016). Mixtures with relatives and linked markers. International journal of legal medicine (Print), 130(3), 621-634
Open this publication in new window or tab >>Mixtures with relatives and linked markers
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2016 (English)In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 130, no 3, p. 621-634Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
SPRINGER, 2016
Keywords
DNA mixtures; Kinship; Linkage; Linkage disequilibrium; Likelihood ratio; Forensics
National Category
Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-128144 (URN)10.1007/s00414-015-1288-x (DOI)000374306800004 ()26614310 (PubMedID)
Available from: 2016-05-19 Created: 2016-05-19 Last updated: 2017-11-30
Kling, D., Tillmar, A., Egeland, T. & Mostad, P. (2015). A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations. International journal of legal medicine (Print), 129(5), 943-954
Open this publication in new window or tab >>A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations
2015 (English)In: International journal of legal medicine (Print), ISSN 0937-9827, E-ISSN 1437-1596, Vol. 129, no 5, p. 943-954Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
SPRINGER, 2015
Keywords
FamLinkX; Lander-Green; Likelihood computations; X chromosome; Markov-chain; Linkage disequilibrium; Linkage; Mutation
National Category
Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-121429 (URN)10.1007/s00414-014-1117-7 (DOI)000360315900003 ()25425094 (PubMedID)
Available from: 2015-09-18 Created: 2015-09-18 Last updated: 2017-12-04
Kling, D., DellAmico, B. & Tillmar, A. (2015). FamLinkX - implementation of a general model for likelihood computations for X-chromosomal marker data. Forensic Science International: Genetics, 17
Open this publication in new window or tab >>FamLinkX - implementation of a general model for likelihood computations for X-chromosomal marker data
2015 (English)In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 17Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2015
Keywords
Linkage; X chromosome; FamLinkX; Linkage disequilibrium; Mutations
National Category
Clinical Medicine
Identifiers
urn:nbn:se:liu:diva-120034 (URN)10.1016/j.fsigen.2015.02.007 (DOI)000355918400001 ()25771099 (PubMedID)
Available from: 2015-07-06 Created: 2015-07-06 Last updated: 2017-12-04
Tillmar, A. O. & Mostad, P. (2014). Choosing supplementary markers in forensic casework. Forensic Science International: Genetics, 13, 128-133
Open this publication in new window or tab >>Choosing supplementary markers in forensic casework
2014 (English)In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 13, p. 128-133Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2014
Keywords
Decision making; Error rate; Paternity testing; Simulation
National Category
Other Medical Sciences
Identifiers
urn:nbn:se:liu:diva-111593 (URN)10.1016/j.fsigen.2014.06.019 (DOI)000342444400026 ()25113577 (PubMedID)
Available from: 2014-10-27 Created: 2014-10-27 Last updated: 2017-12-05
Kling, D., Tillmar, A. O. & Egeland, T. (2014). Familias 3-Extensions and new functionality. Forensic Science International: Genetics, 13, 121-127
Open this publication in new window or tab >>Familias 3-Extensions and new functionality
2014 (English)In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 13, p. 121-127Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
Elsevier, 2014
Keywords
Familias; Paternity; Likelihood computations; Simulation; Mutation; Disaster victim identification
National Category
Other Medical Sciences
Identifiers
urn:nbn:se:liu:diva-111592 (URN)10.1016/j.fsigen.2014.07.004 (DOI)000342444400025 ()25113576 (PubMedID)
Note

Funding Agencies|European Union [285487]

Available from: 2014-10-27 Created: 2014-10-27 Last updated: 2017-12-05
Ballantyne, K. N., Ralf, A., Aboukhalid, R., Achakzai, N. M., Anjos, M. J., Ayub, Q., . . . Kayser, M. (2014). Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats. Human Mutation, 35(8), 1021-1032
Open this publication in new window or tab >>Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats
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2014 (English)In: Human Mutation, ISSN 1059-7794, E-ISSN 1098-1004, Vol. 35, no 8, p. 1021-1032Article in journal (Refereed) Published
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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2014
Keywords
Y-chromosome; Y-STRs; haplotypes; RM Y-STRs; paternal lineage; forensic
National Category
Forensic Science Cell and Molecular Biology
Identifiers
urn:nbn:se:liu:diva-109584 (URN)10.1002/humu.22599 (DOI)000339431600016 ()24917567 (PubMedID)
Available from: 2014-08-21 Created: 2014-08-21 Last updated: 2018-01-11
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