| 1. |
- A.O., Tillmar, et al.
(författare)
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Using X-chromosomal markers in relationship testing: Calculation of likelihood ratios taking both linkage and linkage disequilibrium into account
- 2011
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Ingår i: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 5:5, s. 506-511
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Tidskriftsartikel (refereegranskat)abstract
- X-chromosomal markers in forensic genetics have become more widely used during recent years, particularly for relationship testing. Linkage and linkage disequilibrium (LD) must typically be accounted for when using close X-chromosomal markers. Thus, when producing the weight-of-evidence, given by a DNA-analysis with markers that are linked, the normally used product rule is invalid. Here we present an implementation of an efficient model for calculating likelihood ratios (LRs) with markers on the X-chromosome which are linked and in LD. Furthermore, the model was applied on several cases based on data from the eight X-chromosomal loci included in the Mentype® Argus X-8 (Biotype). Using a simulation approach we showed that the use of X-chromosome data can offer valuable information for choosing between the alternatives in each of the cases we studied, and that the LR can be high in several cases. We demonstrated that when linkage and LD were disregarded, as opposed to taken into account, the difference in calculated LRs could be considerable. When these differences were large, the estimated haplotype frequencies often had a strong impact and we present a method to estimate haplotype frequencies. Our conclusion is that linkage and LD should be accounted for when using the tested set of markers, and the used model is an efficient way of doing so.
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| 2. |
- Albinsson, Linda, et al.
(författare)
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Swedish population data and concordance for the kits PowerPlexÒ ESX 16 System, PowerPlexÒ ESI 16 System, AmpFlSTRÒ NGMTM, AmpFlSTRÒ SGM PlusTM and Investigator ESSplex
- 2011
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Ingår i: Forensic Science International. - Clare, Irland : Elsevier. - 1872-4973 .- 1878-0326. ; 5:3, s. e89-e92
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The European Standard Set of loci (ESS) has been extended with five additional short tandem repeat (STR) loci following the recommendations of the European Network of Forensic Science Institutes (ENFSI) and the European DNA Profiling Group (EDNAP) to increase the number of loci routinely used by the European forensic community. Subsequently, a new extended Swedish population database, based on 425 individuals, has been assembled using the new STR multiplex kits commercially available.Allele frequencies and statistical parameters of forensic interest for 15 autosomal STR loci (D3S1358, TH01, D21S11, D18S51, D10S1248, D1S1656, D2S1338, D16S539, D22S1045, vWA, D8S1179, FGA, D2S441, D12S391 and D19S433) were obtained from the analysis of the PowerPlex® ESX 16 System kit (Promega Corporation, USA). According to the data no evidence of deviations from Hardy–Weinberg equilibrium was found. The observed heterozygosity varies between 0.755 (TH01) and 0.892 (D1S1656). The power of discrimination was smallest for D22S1045 (0.869) and largest for D1S1656 (0.982) while the power of exclusion was smallest for TH01 (0.518) and largest for D1S1656 (0.778).A concordance study was performed on the five amplification systems: PowerPlex® ESX 16 System, PowerPlex® ESI 16 System (Promega Corporation, USA), AmpFlSTR® NGM™, AmpFlSTR® SGM Plus™ (Applied Biosystems, USA) and Investigator ESSplex (Qiagen, Germany) to reveal null alleles and other divergences between the kits. For the 425 DNA profiles included, AmpFlSTR® NGM™ revealed two null alleles, AmpFlSTR® SGM Plus™ revealed one, and Investigator ESSplex revealed a micro-variant, while the rest of the alleles showed full concordance between the kits tested.
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| 3. |
- Chaitanya, Lakshmi, et al.
(författare)
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Collaborative EDNAP exercise on the IrisPlex system for DNA based prediction of human eye colour
- 2014
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 11, s. 241-251
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Tidskriftsartikel (refereegranskat)abstract
- The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average, >94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organised by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising laboratory and judged; 96% of the eye colour phenotypes were inferred correctly across 100 samples and 19 laboratories. The high success rates in genotyping and eye colour phenotyping clearly demonstrate the reproducibility and the robustness of the IrisPlex assay as well as the accuracy of the IrisPlex model to predict blue and brown eye colour from DNA. Additionally, this study demonstrates the ease with which the IrisPlex system is implementable and applicable across forensic laboratories around the world with varying pre-existing experiences.
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| 4. |
- Divne, Anna-Maria, et al.
(författare)
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Forensic analysis of autosomal STR markers using Pyrosequencing
- 2010
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Ingår i: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 4:2, s. 122-129
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Tidskriftsartikel (refereegranskat)abstract
- Short tandem repeats (STRs) are highly variable, and therefore routinely used in forensic investigations for a DNA-based individual identification. The routine assay is commonly performed by size separation using capillary electrophoresis, but alternative technologies can also be used. In this study, a Pyrosequencing assay was developed for analysis of STR markers useful in forensic DNA analysis. The assay was evaluated for 10 different STR loci (CSF1PO, TH01, TPOX, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539 and Penta E) and a total of 114 Swedish individuals were genotyped. This genotyping strategy reveal the actual sequence and variant alleles were seen at several loci, providing additional information compared to fragment size analysis. At the D13S317 locus a T/A SNP located in the last repeat unit was observed in 92% of the genotypes. Moreover, an upstream flanking SNP at locus D7S820, a SNP within the repeats at D3S1358 and D8S1179 and a deletion in the flanking region at locus D5S818 were observed. The Pyrosequencing method was first developed for SNP typing and sequencing of shorter DNA fragments but the method also provides an alternative method for STR analysis of less complex repeats. This assay is suitable for investigation of new markers, a rapid compilation of population data and for confirmation of variant and new alleles.
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| 5. |
- Hedman, Johannes, et al.
(författare)
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Evaluation of amylase testing as a tool for saliva screening of crime scene trace swabs
- 2011
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Ingår i: FORENSIC SCIENCE INTERNATIONAL-GENETICS. - : ELSEVIER IRELAND LTD, ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO, CLARE, 00000, IRELAND. - 1872-4973 .- 1878-0326. ; 5:3, s. 194-198
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Tidskriftsartikel (refereegranskat)abstract
- Amylase testing has been used as a presumptive test for crime scene saliva for over three decades, mainly to locate saliva stains on surfaces. We have developed a saliva screening application for crime scene trace swabs, utilising an amylase sensitive paper (Phadebas (R) Forensic Press test). Positive results were obtained for all tested dried saliva stains (0.5-32 mu L) with high or intermediate amylase activity (840 and 290 kU/L). Results were typically obtained within 5 min, and all samples that produced DNA profiles were positive. However, salivary amylase activities, as well as DNA concentrations, vary significantly between individuals. We show that there is no correlation between amylase activity and amount of DNA in fresh saliva. Even so, a positive amylase result indicates presence of saliva, and thereby presence of DNA. Amylase testing may be useful for screening in investigations where the number of DNA analyses is limited due to cost, e. g., in volume crime.
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| 6. |
- Kling, Daniel, et al.
(författare)
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DNA microarray as a tool in establishing genetic relatedness-Current status and future prospects
- 2012
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 6:3, s. 322-329
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Tidskriftsartikel (refereegranskat)abstract
- In the past decades, microarray technology has definitely put an edge to the field of genetic research. Our aim was to determine whether single nucleotide polymorphism (SNP) microarrays could be used as a tool in establishing genetic relationships where current molecular genetic methods are not sufficient. We used the Genechip, Affymetrix GenomeWide SNP Array 6.0, which detects more than 900,000 SNP markers dispersed throughout the human genome. The intention was to find a good selection of SNP markers that could be used for statistical evaluation of relatedness in a forensic setting. We conducted pairwise comparisons in the R-package FEST as well as pedigree comparisons in Merlin. Our methods were applied on two separate families, where relationships as distant as 3rd cousins were known. In addition, a question about a possible common ancestry between the two families was tested. Relationships as distant as 2nd cousins could be readily distinguished both from unrelated and other, genetically, closer relationships. This was achieved with a selection of 5774 markers, where each pair of markers was separated by a genetic distance of at least 0.5 cM (centiMorgan). When considering 3rd cousins, and more distant relationships, the number of markers needs to be extended, consequently decreasing the genetic distance between the markers. However, inclusion of a too large number of markers presents new challenges and our results imply that the use of too dense sets of markers always yields the highest probability for the genetically closest relationship hypothesis. Simulations confirm that this is most probably caused by the fact that the computational model assumes linkage equilibrium between markers, a problem that will be further evaluated. Our results do however suggest that SNP-data derived from microarrays are well suited for kinship determination provided linkage disequilibrium is properly accounted for.
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| 7. |
- Kling, Daniel, et al.
(författare)
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Familias 3-Extensions and new functionality
- 2014
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 13, s. 121-127
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 8. |
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| 9. |
- Tillmar, Andreas O., et al.
(författare)
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Choosing supplementary markers in forensic casework
- 2014
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Ingår i: Forensic Science International-Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 13, s. 128-133
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 10. |
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