SwePub
Sök i SwePub databas

  Extended search

Träfflista för sökning "L773:1872 4973 "

Search: L773:1872 4973

  • Result 1-50 of 66
Sort/group result
   
EnumerationReferenceCoverFind
1.
  • A.O., Tillmar, et al. (author)
  • Using X-chromosomal markers in relationship testing: Calculation of likelihood ratios taking both linkage and linkage disequilibrium into account
  • 2011
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 5:5, s. 506-511
  • Journal article (peer-reviewed)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.
  •  
2.
  • Adolfsson, Emma, 1977-, et al. (author)
  • Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death
  • 2021
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 53
  • Journal article (peer-reviewed)abstract
    • Sudden cardiac death (SCD) is a tragic and traumatic event. SCD is often associated with hereditary genetic disease and in such cases, sequencing of stored formalin fixed paraffin embedded (FFPE) tissue is often crucial in trying to find a causal genetic variant. This study was designed to compare two massive parallel sequencing assays for differences in sensitivity and precision regarding variants related to SCD in FFPE material. From eight cases of SCD where DNA from blood had been sequenced using HaloPlex, corresponding FFPE samples were collected six years later. DNA from FFPE samples were amplified using HaloPlex HS, sequenced on MiSeq, representing the first method, as well as amplified using modified Twist and sequenced on NextSeq, representing the second method. Molecular barcodes were included to distinguish artefacts from true variants. In both approaches, read coverage, uniformity and variant detection were compared using genomic DNA isolated from blood and corresponding FFPE tissue, respectively. In terms of coverage uniformity, Twist performed better than HaloPlex HS for FFPE samples. Despite higher overall coverage, amplicon-based HaloPlex technologies, both for blood and FFPE tissue, suffered from design and/or performance issues resulting in genes lacking complete coverage. Although Twist had considerably lower overall mean coverage, high uniformity resulted in equal or higher fraction of genes covered at ≥ 20X. By comparing variants found in the matched samples in a pre-defined cardiodiagnostic gene panel, HaloPlex HS for FFPE material resulted in high sensitivity, 98.0% (range 96.6-100%), and high precision, 99.9% (range 99.5-100%) for moderately fragmented samples, but suffered from reduced sensitivity (range 74.2-91.1%) in more severely fragmented samples due to lack of coverage. Twist had high sensitivity, 97.8% (range 96.8-98.7%) and high precision, 99.9% (range 99.3-100%) in all analyzed samples, including the severely fragmented samples.
  •  
3.
  • Albinsson, Linda, et al. (author)
  • 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
  • In: Forensic Science International. - Clare, Irland : Elsevier. - 1872-4973 .- 1878-0326. ; 5:3, s. e89-e92
  • Journal article (other academic/artistic)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.
  •  
4.
  • Anderung, Cecilia, et al. (author)
  • Fishing for ancient DNA
  • 2008
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973. ; 2:2, s. 104-107
  • Journal article (peer-reviewed)abstract
    • The major problems concerning ancient DNA studies are related to the amount of extractable DNA and the precautions needed to avoid contamination. From the very first step of the analyses, the DNA extraction, these problems must be confronted. There are several extraction methods available for DNA in ancient tissue; several of them are complicated and time consuming. and none of the methods have reached an acceptance level such that they are routinely used on a widespread basis. Here we investigate the efficiency of two methods. one based on magnetic separation of the targeted molecules. and one based oil silica binding. The efficiency rate of these two on the material studied seems to be identical. The silica binding method has the benefit of relative simplicity, but the magnetic separation technique also hits advantages. For example, it is possible to reuse the extract several times for different loci, and it is possible to concentrate all extracted DNA from one locus into one PCR.
  •  
5.
  • Andréasson, Hanna, et al. (author)
  • Forensic mitochondrial coding region analysis for increased discrimination using pyrosequencing technology
  • 2007
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 1:1, s. 35-43
  • Journal article (peer-reviewed)abstract
    • Analysis of mitochondrial DNA (mtDNA) is very useful when nuclear DNA analysis fails due to degradation or insufficient amounts of DNA in forensic analysis. However, mtDNA analysis has a lower discrimination power compared to what can be obtained by nuclear DNA (nDNA) analysis, potentially resulting in multiple individuals showing identical mtDNA types in the HVI/HVII region. In this study, the increase in discrimination by analysis of mitochondrial coding regions has been evaluated for identical or similar HVI/HVII sequences. A pyrosequencing-based system for coding region analysis, comprising 17 pyrosequencing reactions performed on 15 PCR fragments, was utilised. This assay was evaluated in 135 samples, resulting in an average read length of 81 nucleotides in the pyrosequencing analysis. In the sample set, a total of 52 coding region SNPs were identified, of which 18 were singletons. In a group of 60 samples with 0 or 1 control region difference from the revised Cambridge reference sequence (rCRS), only 12 samples could not be resolved by at least two differences using the pyrosequencing assay. Thus, the use of this pyrosequencing-based coding region assay has the potential to substantially increase the discriminatory power of mtDNA analysis.
  •  
6.
  • Bergseth, Erik F., et al. (author)
  • Extended population genetic analysis of 12 X-STRs - Exemplified using a Norwegian population sample
  • 2022
  • In: Forensic Science International. - : Elsevier Ireland Ltd. - 1872-4973 .- 1878-0326. ; 60
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
7.
  •  
8.
  • Bouakaze, Caroline, et al. (author)
  • Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex) : Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters
  • 2020
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 48
  • Journal article (peer-reviewed)abstract
    • We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
  •  
9.
  • Bus, Magdalena M., et al. (author)
  • Mitochondrial DNA analysis of a Viking age mass grave in Sweden
  • 2019
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 42, s. 268-274
  • Journal article (peer-reviewed)abstract
    • In 1998, a Viking Age mass grave was discovered and excavated at St. Laurence's churchyard in Sigtuna, Sweden. The excavated bones underwent osteoarchaeological analysis and were assigned to at least 19 individuals. Eleven skeletons showed sharp force trauma from bladed weapons. Mass graves are an unusual finding from this time period, making the burial context extraordinary. To investigate a possible maternal kinship among the individuals, bones and teeth from the skeletal remains were selected for mitochondrial DNA (mtDNA) analysis. Sanger sequencing of short stretches of the hypervariable segments I and II (HVS-I and HVS-II) was performed. A subset of the samples was also analysed by massively parallel sequencing analysis (MPS) of the entire mtDNA genome using the Precision ID mtDNA Whole Genome Panel. A total of 15 unique and three shared mtDNA profiles were obtained. Based on a combination of genetic and archaeological data, we conclude that a minimum of 20 individuals was buried in the mass grave. The majority of the individuals were not maternally related. However, two possible pairs of siblings or mother-child relationships were identified. All individuals were assigned to West Eurasian haplogroups, with a predominance of haplogroup H. Although the remains showed an advanced level of DNA degradation, the combined use of Sanger sequencing and MPS with the Precision ID mtDNA Whole Genome Panel revealed at least partial mtDNA data for all samples.
  •  
10.
  • Chaitanya, Lakshmi, et al. (author)
  • Collaborative EDNAP exercise on the IrisPlex system for DNA based prediction of human eye colour
  • 2014
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 11, s. 241-251
  • Journal article (peer-reviewed)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.
  •  
11.
  • Divne, Anna-Maria, et al. (author)
  • Forensic analysis of autosomal STR markers using Pyrosequencing
  • 2010
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 4:2, s. 122-129
  • Journal article (peer-reviewed)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.
  •  
12.
  • Dwibedi, Chinmay Kumar, et al. (author)
  • Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis
  • 2020
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 45
  • Journal article (peer-reviewed)abstract
    • Challenges of investigating a suspected bio attack include establishing if microorganisms have been cultured to produce attack material and to identify their source. Addressing both issues, we have investigated genetic variations that emerge during laboratory culturing of the bacterial pathogen Francisella tularensis. Key aims were to identify genetic variations that are characteristic of laboratory culturing and explore the possibility of using biological amplification to identify genetic variation present at exceedingly low frequencies in a source sample. We used parallel serial passage experiments and high-throughput sequencing of F. tularensis to explore the genetic variation. We found that during early laboratory culture passages of F. tularensis, gene duplications emerged in the pathogen genome followed by single-nucleotide polymorphisms in genes for bacterial capsule synthesis. Based on a biological enrichment scheme and the use of high-throughput sequencing, we identified genetic variation that likely pre-existed in a source sample. The results support that capsule synthesis gene mutations are common during laboratory culture, and that a biological amplification strategy is useful for linking a F. tularensis sample to a specific laboratory variant among many highly similar variants.
  •  
13.
  • Dåderman, Anna, et al. (author)
  • The importance of a urine sample in persons intoxicated with flunitrazepam : legal issues in a forensic psychiatric case study of a serial murderer
  • 2003
  • In: Forensic Science International. - Göttingen : Elsevier. - 0379-0738 .- 1872-6283. ; 137:1, s. 21-27
  • Journal article (peer-reviewed)abstract
    • The sedative–hypnotic benzodiazepine flunitrazepam (FZ) is abused worldwide. The purpose of our study was to investigate violence and anterograde amnesia following intoxication with FZ, and how this was legally evaluated in forensic psychiatric investigations with the objective of drawing some conclusions about the importance of urine sample in a case of a suspected intoxication with FZ. The case was a 23-year-old male university student who, intoxicated with FZ (and possibly with other substances such as diazepam, amphetamines or cannabis), first stabbed an acquaintance and, 2 years later, two friends to death. The police investigation files, including video-typed interviews, the forensic psychiatric files, and also results from the forensic autopsy of the victims, were compared with the information obtained from the case. Only partial recovery from anterograde amnesia was shown during a period of several months. Some important new information is contained in this case report: a forensic analysis of blood sample instead of a urine sample, might lead to confusion during police investigation and forensic psychiatric assessment (FPA) of an FZ abuser, and in consequence wrong legal decisions. FZ, alone or combined with other substances, induces severe violence and is followed by anterograde amnesia. All cases of bizarre, unexpected aggression followed by anterograde amnesia should be assessed for abuse of FZ. A urine sample is needed in case of suspected FZ intoxication. The police need to be more aware of these issues, and they must recognise that they play a crucial role in an assessment procedure. Declaring FZ an illegal drug is strongly recommended.
  •  
14.
  • Edlund, Hanna, et al. (author)
  • Y chromosomal STR analysis using Pyrosequencing technology
  • 2009
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 3:2, s. 119-124
  • Journal article (peer-reviewed)abstract
    • Analysis of Y chromosome STR markers has proven to be useful in forensic cases where the samples contain a mixture of DNA from several individuals. STR markers are commonly genotyped based on length separation of PCR products. In this study we evaluated if Pyrosequencing can be used as an alternative method for determining Y-STR variants. In total 70 unrelated Swedish males were typed for the Y chromosomal markers (DYS19, DYS389 I-II, DYS390, DYS391, DYS392, DYS393 and DYS438) using Pyrosequencing. Using the 8 markers, 57 unique haplotypes were observed with a discrimination capacity of 0.81. At four loci, the Pyrosequencing analysis revealed sequence variants. The sequence variants were found in the DYS389 II, DYS390, DYS391, and DYS393 loci in frequencies between 1.43% and 14.3%. Pyrosequencing has here been shown to be a useful tool for typing Y chromosomal STRs and the method can provide a complement to conventional forensic Y STR analyses. Moreover, the Pyrosequencing method can be used to rapidly evaluate novel markers.
  •  
15.
  • Fernlund, Eva, et al. (author)
  • The congenital disorder of glycosylation in PGM1 (PGM1-CDG) can cause severe cardiomyopathy and unexpected sudden cardiac death in childhood
  • 2019
  • In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 43
  • Journal article (peer-reviewed)abstract
    • Introduction: Sudden cardiac death (SCD) in the young is rare and should always lead to suspicion of a genetic cardiac disorder. We describe a family, in which the proband was a girl deceased by sudden cardiac death in the playground at thirteen years of age. The index-patient had short stature, cleft palate but no previous cardiac symptoms. We found an uncommon cause of cardiomyopathy, due to a congenital disorder of glycosylation (CDG), previously described to cause a variable range of usually mild symptoms, and not previously found to cause SCD as the first symptom of the condition. Methods: The index patient underwent postmortem genetic testing/molecular autopsy for genes known to cause SCD, without a detection of causative agent, why two siblings of similar phenotype as the deceased sister underwent clinical-exome genetic sequencing (next generation sequencing). All first-degree relatives underwent clinical examination including cardiac ultrasound, Holzer-ECG, exercise stress test and biochemistry panel. Results: A genetic variant in the gene for phosphoglucomutase 1 (PGM1) was identified in the index patient and her two brothers, all were found to be homozygous for the genetic variant (G230E) NM_002633.2:c.689 G amp;gt; A in PGM1. This variant has been linked to a congenital disorder of glycosylation (PGM1-CDG), explaining the clinical picture of short stature, cleft palate, liver engagement and cardiomyopathy. During follow-up one of the brothers died unexpectedly after physical exertion during daily life at the age of twelve years. The other brother fainted during similar circumstances at the age of thirteen years. Both parents and three other siblings were found to be heterozygous gene carriers without risk for the disease. Conclusion: Our findings suggest that there is a need of multidisciplinary discussion and genetic testing after unexpected cardiac death in the young. We have to be more flexible in our evaluation of diseases and to consider even uncommon diseases including rare recessive inherited disorders. Our findings also suggest that the autosomal recessive PGM1-CDG might be highly associated with life-threatening cardiomyopathy with arrhythmia or sudden cardiac death as the first symptom presenting from childhood and adolescence.
  •  
16.
  • Foreberg, Christina, et al. (author)
  • High-throughput DNA extraction of forensic adhesive tapes
  • 2016
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 24, s. 158-163
  • Journal article (peer-reviewed)abstract
    • Tape-lifting has since its introduction in the early 2000's become a well-established sampling method in forensic DNA analysis. Sampling is quick and straightforward while the following DNA extraction is more challenging due to the "stickiness", rigidity and size of the tape. We have developed, validated and implemented a simple and efficient direct lysis DNA extraction protocol for adhesive tapes that requires limited manual labour. The method uses Chelex beads and is applied with SceneSafe FAST tape. This direct lysis protocol provided higher mean DNA yields than PrepFiler Express BTA on Automate Express, although the differences were not significant when using clothes worn in a controlled fashion as reference material (p=0.13 and p=0.34 for T-shirts and button-down shirts, respectively). Through in-house validation we show that the method is fit-for-purpose for application in casework, as it provides high DNA yields and amplifiability, as well as good reproducibility and DNA extract stability. After implementation in casework, the proportion of extracts with DNA concentrations above 0.01ng/μL increased from 71% to 76%. Apart from providing higher DNA yields compared with the previous method, the introduction of the developed direct lysis protocol also reduced the amount of manual labour by half and doubled the potential throughput for tapes at the laboratory. Generally, simplified manual protocols can serve as a cost-effective alternative to sophisticated automation solutions when the aim is to enable high-throughput DNA extraction of complex crime scene samples.
  •  
17.
  • Gorden, Erin M., et al. (author)
  • Capture enrichment and massively parallel sequencing for human identification
  • 2021
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 53
  • Research review (peer-reviewed)abstract
    • In the past decade, hybridization capture has gained attention within the forensic field for its possible use in human identification. One of the primary benefits to capture enrichment is its applicability to degraded DNA fragments that, due to their reduced size, are not amenable to traditional PCR enrichment techniques. Hybridization capture is typically introduced after genomic library preparation of extracted DNA templates for the subsequent enrichment of mitochondrial DNA or single nucleotide polymorphisms within the nuclear genome. The enriched molecules are then subjected to massively parallel sequencing (MPS) for sensitive and highthroughput DNA sequence generation. Bioinformatic analysis of capture product removes PCR duplicates that were introduced during the laboratory workflow in order to characterize the original DNA template molecules. In the case of aged and degraded skeletal remains, the fraction of endogenous human DNA may be very low; therefore low-coverage sequence analysis may be required. This review contains an overview of current capture methodologies and the primary literature on hybridization capture as evaluated for forensic applications.
  •  
18.
  • Gorden, Erin M., et al. (author)
  • Extended kinship analysis of historical remains using SNP capture
  • 2022
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 57
  • Journal article (peer-reviewed)abstract
    • DNA-assisted identification of historical remains requires the genetic analysis of highly degraded DNA, along with a comparison to DNA from known relatives. This can be achieved by targeting single nucleotide polymorphisms (SNPs) using a hybridization capture and next-generation sequencing approach suitable for degraded skeletal samples. In the present study, two SNP capture panels were designed to target similar to 25,000 (25 K) and similar to 95,000 (95 K) nuclear SNPs, respectively, to enable distant kinship estimation (up to 4th degree relatives). Low-coverage SNP data were successfully recovered from 14 skeletal elements 75 years postmortem using an Illumina MiSeq benchtop sequencer. All samples contained degraded DNA but were of varying quality with mean fragment lengths ranging from 32 bp to 170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fx Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with cytosine deamination. The 25 K panel produced 15,000 SNPs on average, which allowed for accurate kinship prediction with strong statistical support in 16 of the 21 pairwise comparisons. The 95 K panel increased the average SNPs to 42,000 and resulted in an additional accurate kinship prediction with strong statistical support (17 of 21 pairwise comparisons). This study demonstrates that SNP capture combined with massively parallel sequencing on a benchtop platform can yield sufficient SNP recovery from compromised samples, enabling accurate, extended kinship predictions.
  •  
19.
  • Hedell, Ronny, 1985, et al. (author)
  • Enhanced low-template DNA analysis conditions and investigation of allele dropout patterns
  • 2015
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1878-0326 .- 1872-4973. ; 14, s. 61-75
  • Journal article (peer-reviewed)abstract
    • Forensic DNA analysis applying PCR enables profiling of minute biological samples. Enhanced analysis conditions can be applied to further push the limit of detection, coming with the risk of visualising artefacts and allele imbalances. We have evaluated the consecutive increase of PCR cycles from 30 to 35 to investigate the limitations of low-template (LT) DNA analysis, applying the short tandem repeat (STR) analysis kit PowerPlex ESX 16. Mock crime scene DNA extracts of four different quantities (from around 8-84 pg) were tested. All PCR products were analysed using 5, 10 and 20 capillary electrophoresis (CE) injection seconds. Bayesian models describing allele dropout patterns, allele peak heights and heterozygote balance were developed to assess the overall improvements in EPG quality with altered PCR/CE settings. The models were also used to evaluate the impact of amplicon length, STR marker and fluorescent label on the risk for allele dropout. The allele dropout probability decreased for each PCR cycle increment from 30 to 33 PCR cycles. Irrespective of DNA amount, the dropout probability was not affected by further increasing the number of PCR cycles. For the 42 and 84 pg samples, mainly complete DNA profiles were generated applying 32 PCR cycles. For the 8 and 17 pg samples, the allele dropouts decreased from 100% using 30 cycles to about 75% and 20%, respectively. The results for 33, 34 and 35 PCR cycles indicated that heterozygote balance and stutter ratio were mainly affected by DNA amount, and not directly by PCR cycle number and CE injection settings. We found 32 and 33 PCR cycles with 10 CE injection seconds to be optimal, as 34 and 35 PCR cycles did not improve allele detection and also included CE saturation problems. We find allele dropout probability differences between several STR markers. Markers labelled with the fluorescent dyes CXR-ET (red in electropherogram) and TMR-ET (shown as black) generally have higher dropout risks compared with those labelled with JOE (green) and fluorescein (blue). Overall, the marker D10S1248 has the lowest allele dropout probability and D8S1179 the highest. The marker effect is mainly pronounced for 30-32 PCR cycles. Such effects would not be expected if the amplification efficiencies were identical for all markers. Understanding allele dropout risks and the variability in peak heights and balances is important for correct interpretation of forensic DNA profiles.
  •  
20.
  • Hedman, Johannes, et al. (author)
  • A fast analysis system for forensic DNA reference samples
  • 2008
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1878-0326 .- 1872-4973. ; 2:3, s. 184-189
  • Journal article (peer-reviewed)abstract
    • On January 1st, 2006, the Swedish legislation on obtaining DNA reference samples from Suspects and the recording of DNA profiles in databases was changed. As a result the number of samples analysed at the Swedish National Laboratory of Forensic Science (SKL) increased from about 4500 in 2005 to more than 25,000 in 2006. To meet this challenge, SKL launched a flew analysis system to create an unbroken chain, from sampling to incorporation of a profile in the national DNA database and subsequent automatic generation of digitally signed hit reports. The system integrates logistics, digital data transfer, new functions in LIMS (ForumDNA Version 4, Ida Infront AB) and laboratory automation. Buccal swab samples are secured on a FTA (R) card attached to an identity form, which is barcoded with a unique sample ID. After sampling, the police officer sends a digital request to SKL. The sample is automatically registered in LIMS and processed on delivery. The resulting DNA profiles are automatically classified according to quality using a custom-made expert system. Building the evaluation around mathematical rules makes it reproducible, standardised and minimises manual work and clerk errors. All samples are run in duplicate and the two profiles are compared within LIMS before incorporation in the database. In the first year of operation, the median time for completion of an analysis was 3 days, measured from delivery of the sample to incorporation of the profile in the national DNA database. In spite of the dramatic increase in the number of reference samples there was no backlog. (C) 2008 Elsevier Ireland Ltd. All rights reserved.
  •  
21.
  • Hedman, Johannes, et al. (author)
  • Enhanced forensic DNA recovery with appropriate swabs and optimized swabbing technique
  • 2021
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 53
  • Journal article (peer-reviewed)abstract
    • Efficient sampling with swabs is crucial for optimal forensic DNA analysis. The DNA recovery is determined by the skill of the practitioner and the compatibility between the applied swab and the surface. Here we investigate the impact of swabbing technique and swab type on the DNA yield. Thirteen different swabs from four categories (cotton, flocked nylon, small foam and large foam) provided equal DNA yields for smooth/non-absorbing surfaces. Large foam swabs gave higher DNA recovery for an absorbing wood surface. Factorial design of experiments and ANOVA was applied to study swabbing techniques for cotton swabs. Two key factors for efficient sampling were found to be 1) holding the swab with an approximate 60° angle against the surface and 2) to rotate the swab during sampling. For absorbing wood, it was beneficial to wet the swab heavily. The results of the factorial experiments were used to develop swabbing protocols for different surfaces. When ten experienced practitioners sampled according to these protocols, the DNA yield was increased for ridged plastic (around 1.25 times more DNA) and absorbing wood (2.2–6.2 times more DNA). For window glass, representing a smooth/non-absorbing surface, sampling according to the protocol gave DNA yields equivalent to applying individual sampling techniques. The protocol lowered person-to-person variation for ridged plastic. In conclusion, we have developed instructive protocols for cotton swab sampling on three types of surfaces: smooth/non-absorbing, ridged/non-absorbing and smooth/absorbing. We believe that such swabbing protocols will streamline and simplify the training of new practitioners and improve sampling efficiency for invisible DNA residues in casework.
  •  
22.
  • Hedman, Johannes, et al. (author)
  • Evaluation of amylase testing as a tool for saliva screening of crime scene trace swabs
  • 2011
  • In: 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
  • Journal article (peer-reviewed)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.
  •  
23.
  • Hedman, Johannes, et al. (author)
  • The double-swab technique versus single swabs for human DNA recovery from various surfaces
  • 2020
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 46
  • Journal article (peer-reviewed)abstract
    • Most crime scene DNA evidence is retrieved using cotton swabs. Since the late 90’s, the double-swab technique has been favoured by many practitioners throughout the world. However, the superiority of double-swabbing over applying single wet swabs has not been broadly verified. Here we set out to evaluate the need for the second dry swab for various surfaces, aiming at mimicking the range of surfaces encountered at crime scenes: flat and ridged, absorbing and non-absorbing. For the tested non-absorbing surfaces, i.e., window glass, steel, brass, synthetic leather and ridged plastic, the first wet swabs gave at least 16 times higher DNA yields compared to the second dry swabs. In addition, second wet swabs gave more DNA than second dry ones, opposing the common notion that the purpose of the second swab is to absorb excess liquid. When ten experienced staff members sampled saliva stains on a window glass surface the variation between persons was considerable, with mean DNA yields for the first wet swabs ranging from 0.045 ± 0.022 to 0.13 ± 0.024 ng/μL. The first wet swabs gave 4–162 times more DNA than the second dry swabs, with higher DNA amounts on second swabs coinciding with lower amounts for first swabs. We show that for non-absorbing surfaces, the first wet swab takes up most of the cells in dried stains, making it less valuable to apply a second dry swab. The differences in DNA recovery between first and second swabs were notable also for absorbing surfaces. Double-swabbing may be preferable for some complex surfaces, but focusing on efficient sampling technique with single wet swabs is likely a better general approach.
  •  
24.
  • Heidegger, A., et al. (author)
  • Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis
  • 2022
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973. ; 56
  • Journal article (peer-reviewed)abstract
    • The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority from blood. Age prediction from semen requires different DNA methylation markers and the only assays currently developed for forensic analysis are based on SNaPshot or pyrosequencing. Here, we describe a new assay using massively parallel sequencing to analyse 13 candidate CpG sites targeted in two multiplex PCRs. The assay has been validated by five consortium laboratories of the VISible Attributes through GEnomics (VISAGE) project within a collaborative exercise and was tested for reproducible quantification of DNA methylation levels and sensitivity with DNA methylation controls. Furthermore, DNA extracts and stains on Whatman FTA cards from two semen samples were used to evaluate concordance and mimic casework samples. Overall, the assay yielded high read depths (> 1000 reads) at all 13 marker positions. The methylation values obtained indicated robust quantification with an average standard deviation of 2.8% at the expected methylation level of 50% across the 13 markers and a good performance with 50 ng DNA input into bisulfite conversion. The absolute difference of quantifications from one participating laboratory to the mean quantifications of concordance and semen stains of remaining laboratories was approximately 1%. These results demonstrated the assay to be robust and suitable for age estimation from semen in forensic investigations. In addition to the 13-marker assay, a more streamlined protocol combining only five age markers in one multiplex PCR was developed. Preliminary results showed no substantial differences in DNA methylation quantification between the two assays, indicating its applicability with the VISAGE age model for semen developed with data from the complete 13-marker tool.
  •  
25.
  • Jakobsson, Gerd, et al. (author)
  • Oxycodone findings and CYP2D6 function in postmortem cases
  • 2021
  • In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 53
  • Journal article (peer-reviewed)abstract
    • Genetic disposition can cause variation in oxycodone pharmacokinetic characteristics and decrease or increase the expected clinical response. In forensic medicine, determination of cause of death or assessing time between drug intake and death can be facilitated by knowledge of parent and metabolite concentrations. In this study, the aim was to investigate if CYP2D6 genotyping can facilitate interpretation by investigating the frequency of the four CYP2D6 phenotypes, poor metabolizer, intermediate metabolizer, extensive metabolizer, and ultra-rapid metabolizer in postmortem cases, and to study if the CYP2D6 activity was associated with a certain cause of death, concentration, or metabolic ratio. Cases positive for oxycodone in femoral blood (n = 174) were genotyped by pyrosequencing for CYP2D6*3, *4, and *6 and concentrations of oxycodone, noroxycodone, oxymorphone, and noroxymorphone were determined by LC-MS/MS (LLOQ 0.005 mu g/g). Digital droplet PCR was used to determine the copy number variation for CYP2D6*5. Cases were categorized by cause of death. It was found that poor and intermediate CYP2D6 metabolizers had significantly higher oxycodone and noroxycodone concentrations compared to extensive and ultra-rapid metabolizers. CYP2D6 phenotype were equally distributed between cause of death groups, showing that no phenotype was overrepresented in any of the cause of death groups. We also found that the concentration ratio between oxymorphone and oxycodone depended on the CYP2D6 activity when death was unrelated to intoxication. In general, a low metabolite to parent ratio indicate an acute intake. By using receiver operating characteristic (ROC) analysis, we conclude that an oxymorphone/ oxycodone ratio lower than 0.075 has a high sensitivity for separating intoxications with oxycodone from other intoxications and non-intoxications. However, the phenotype needs to be known to reach a high specificity. Therefore, the ratio should not be used as a biomarker on its own to distinguish between different causes of death but needs to be complemented by genotyping.
  •  
26.
  • Jansson, Linda, et al. (author)
  • Assessing the consistency of shedder status under various experimental conditions
  • 2024
  • In: Forensic Science International: Genetics. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 69
  • Journal article (peer-reviewed)abstract
    • Shedder status is defined as the propensity of an individual to leave DNA behind on touched items or surfaces and has been suggested as one of the major factors influencing DNA transfer. However, little is known about whether shedder status is a constant property of an individual across multiple measurements or when the environmental conditions are changed. We have assessed DNA depositions of six males on 20 occasions to acquire a reference data set and to classify the participants into high, intermediate, or low shedders. This data set was also used to investigate how the probability of a correct shedder status classification changed when the number of DNA deposition measurements increased. Individual sweat rates were measured with a VapoMeter and data regarding hygiene routines were collected through a questionnaire on each sampling occasion. Next, we investigated how changes in the experimental conditions such as seasonal variation, hygiene routines, the temperature of the touched object, and repeated handling of an object influenced the DNA shedding. Additionally, we assessed DNA collected from the face and from T-shirts worn by the six participants to explore whether shedder status may be associated with the relative amount of DNA obtained from other body parts. Our results indicate that shedder status is a stable property across different seasons and different temperatures of handled objects. The relative DNA amounts obtained from repeatedly handled tubes, worn T-shirts, and from faces reflected the shedder status of the participants. We suggest that an individual's shedder status is highly influenced by the DNA levels on other body parts than hands, accumulating on the palms by frequently touching e.g., the face or previously handled items harboring self-DNA. Assessing physiological differences between the participants revealed that there were no associations between DNA shedding and individual sweat rates.
  •  
27.
  • Jansson, Linda, et al. (author)
  • Factors affecting DNA recovery from cartridge cases
  • 2020
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 48
  • Journal article (peer-reviewed)abstract
    • Cartridge cases are often the sole items left behind after a shooting incident and DNA traces from these can identify persons connected to the shooting. However, the chance of retrieving usable DNA profiles from cartridge cases is limited, due to the low amounts of deposited DNA and subsequent DNA loss associated with the firing process. In the current study, we set out to increase the DNA recovery from cartridge cases and cartridges by evaluating different swab types and detergents used for trace collection. A protocol applying nylon-flocked swabs instead of cotton swabs was implemented in casework at the Swedish National Forensic Centre (NFC), increasing DNA yield. The number of samples providing a DNA concentration ≥ 0.001 ng/μL (the in-house cut-off for processing low-template samples) increased from 11.1 to 28.6 % for cartridge cases and from 16.0 to 43.3 % for cartridges. There was also a substantial increase in mixed STR profiles, too complex to use for comparisons. Thus, it was not possible to take the full advantage of the elevated DNA yield provided by nylon-flocked swabs. The number of usable STR profiles increased from 5.0 to 8.0 % for cartridge cases and remained unchanged for cartridges. Controlled studies were performed to assess the impact on the DNA recovery from different persons handling the ammunition, different material and size of the cartridge cases, and the type of firearm used. These studies reflected an ideal situation, where all cartridges were extensively handled and loaded without gloves, thus providing a higher expected DNA yield compared to most casework samples. The total peak height differed by up to a factor of ∼50 when 20 different persons handled cartridges prior to shooting. By evaluating eleven combinations of different firearms and ammunition, it was found that the casing material and type of firearm also have a substantial impact on DNA yield.
  •  
28.
  • Jansson, Linda, et al. (author)
  • Individual shedder status and the origin of touch DNA
  • 2022
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 56
  • Journal article (peer-reviewed)abstract
    • Due to improved laboratory techniques, touched surfaces and items are increasingly employed as sources of forensic DNA evidence. This has urged a need to better understand the mechanisms of DNA transfer between individuals. Shedder status (i.e. the propensity to leave DNA behind) has been identified as one major factor regulating DNA transfer. It is known that some individuals tend to shed more DNA than others, but the mechanisms behind shedder status are largely unknown. By comparing the amounts of DNA deposited from active hands (i.e. used “as usual”) and inactive hands (i.e. not allowed to touch anything), we show that some of the self-DNA deposited from hands is likely to have accumulated on hands from other parts of the body or previously handled items (active hands: 2.1 ± 2.7 ng, inactive hands: 0.83 ± 1.1 ng, paired t-test: p = 0.014, n = 27 pairs of hands). Further investigation showed that individual levels of deposited DNA are highly associated with the level of DNA accumulation on the skin of the face (Pearson's correlation: r = 0.90, p < 0.00001 and Spearman's ranked correlation: rs = 0.56, p = 0.0016, n = 29). We hypothesized that individual differences in sebum secretion levels could influence the amount of DNA accumulation in facial areas, but no such correlation was seen (Pearson's correlation: r = − 0.13, p = 0.66, n = 14). Neither was there any correlation between DNA levels on hands or forehead and the time since hand or face wash. We propose that the amount of self-DNA deposited from hands is highly influenced by the individual levels of accumulated facial DNA, and that cells/DNA is often transferred to hands by touching or rubbing one's face.
  •  
29.
  • Juras, Anna, et al. (author)
  • Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA
  • 2017
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 26, s. 30-39
  • Journal article (peer-reviewed)abstract
    • We applied an interdisciplinary approach to investigate kinship patterns and funerary practices during the middle Neolithic. Genetic studies, radiocarbon dating, and taphonomic analyses were used to examine two grave clusters from Krusza Zamkowa, Poland. To reconstruct kinship and determine biological sex, we extracted DNA from bones and teeth, analyzed mitochondrial genomes and nuclear SNPs using the HID-Ion AmpliSeq™ Identity panel generated on Illumina and Ion Torrent platforms, respectively. We further dated the material (AMS 14C) and to exclude aquatic radiocarbon reservoir effects, measures of carbon and nitrogen stable isotopes for diet reconstruction were used. We found distinct mitochondrial genomes belonging to haplogroups U5b2a1a, K1c and H3d in the first grave cluster, and excluded maternal kin patterns among the three analyzed individuals. In the second grave cluster one individual belonged to K1a4. However, we could not affiliate the second individual to a certain haplogroup due to the fragmented state of the mitochondrial genome. Although the individuals from the second grave cluster differ at position 6643, we believe that more data is needed to fully resolve this issue. We retrieved between 26 and 77 autosomal SNPs from three of the individuals. Based on kinship estimations, taking into account the allelic dropout distribution, we could not exclude first degree kin relation between the two individuals from the second grave cluster. We could, however, exclude a first degree kinship between these two individuals and an individual from the first grave cluster. Presumably, not only biological kinship, but also social relations played an important role in the funerary practice during this time period. We further conclude that the HID-Ion AmpliSeq™ Identity Panel may prove useful for first degree kin relation studies for samples with good DNA preservation, and that mitochondrial genome capture enrichment is a powerful tool for excluding direct maternal relationship in ancient individuals.
  •  
30.
  • Kling, Daniel, et al. (author)
  • DNA microarray as a tool in establishing genetic relatedness-Current status and future prospects
  • 2012
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 6:3, s. 322-329
  • Journal article (peer-reviewed)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.
  •  
31.
  • Kling, Daniel, et al. (author)
  • Familias 3-Extensions and new functionality
  • 2014
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 13, s. 121-127
  • Journal article (peer-reviewed)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.
  •  
32.
  • Kling, Daniel, et al. (author)
  • FamLinkX - implementation of a general model for likelihood computations for X-chromosomal marker data
  • 2015
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 17
  • Journal article (peer-reviewed)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.
  •  
33.
  • Kling, Daniel, et al. (author)
  • Forensic genealogy-A comparison of methods to infer distant relationships based on dense SNP data
  • 2019
  • In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 42, s. 113-124
  • Journal article (peer-reviewed)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.
  •  
34.
  • Kling, Daniel, et al. (author)
  • Investigative genetic genealogy : Current methods, knowledge and practice
  • 2021
  • In: Forensic Science International. - : Elsevier Ireland Ltd. - 1872-4973 .- 1878-0326. ; 52
  • Research review (peer-reviewed)abstract
    • 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.
  •  
35.
  • Kokshoorn, Bas, et al. (author)
  • Sharing data on DNA transfer, persistence, prevalence and recovery : Arguments for harmonization and standardization
  • 2018
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 37, s. 260-269
  • Journal article (peer-reviewed)abstract
    • Sharing data between forensic scientists on DNA transfer, persistence, prevalence and recovery (TPPR) is crucial to advance the understanding of these issues in the criminal justice community. We present the results of a collaborative exercise on reporting forensic genetics findings given activity level propositions. This exercise outlined differences in the methodology that was applied by the participating laboratories, as well as limitations to the use of published data on DNA TPPR. We demonstrate how publication of experimental results in scientific journals can be further improved to allow for an adequate use of these data. Steps that can be taken to share and use these data for research and casework purposes are outlined, and the prospects for future sharing of data through publicly accessible databases are discussed. This paper also explores potential avenues to proceed with implementation and is intended to fuel the discussion on sharing data pertaining to DNA TPPR issues. It is further suggested that international standardization and harmonization on these topics will benefit the forensic DNA community as it has been achieved in the past with the harmonization of STR typing systems.
  •  
36.
  • Llobet, Mònica Ortega, et al. (author)
  • Forensic prediction of sex, age, height, body mass index, hip-to-waist ratio, smoking status and lipid lowering drugs using epigenetic markers and plasma proteins
  • 2023
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 65
  • Journal article (peer-reviewed)abstract
    • The prediction of human characteristics from blood using molecular markers would be very helpful in forensic science. Such information can be particularly important in providing investigative leads in police casework from, for example, blood found at crime scenes in cases without a suspect. Here, we investigated the possibilities and limitations of predicting seven phenotypic traits (sex, age, height, body mass index [BMI], hip-to-waist [WTH] ratio, smoking status and lipid-lowering drug use) using either DNA methylation or plasma proteins separately or in combination. We developed a prediction pipeline starting with the prediction of sex followed by sex-specific, stepwise, individual age, sex-specific anthropometric traits and, finally, lifestyle-related traits. Our data revealed that age, sex and smoking status can be accurately predicted from DNA methylation alone, while the use of plasma proteins was highly accurate for prediction of the WTH ratio, and a combined analysis of the best predictions for BMI and lipid-lowering drug use. In unseen individuals, age was predicted with a standard error of 3.3 years for women and 6.5 years for men, while the accuracy in smoking prediction across both men and women was 0.86. In conclusion, we have developed a stepwise approach for the de-novo prediction of individual characteristics from plasma proteins and DNA methylation markers. These models are accurate and may provide valuable information and investigative leads in future forensic casework.
  •  
37.
  • Marshall, Charla, et al. (author)
  • Mitochondrial DNA haplogrouping to assist with the identification of unknown service members from the World War II Battle of Tarawa
  • 2020
  • In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 47
  • Journal article (peer-reviewed)abstract
    • The World War II Battle of Tarawa, 1943, was a devastating conflict that resulted in losses of more than 1100 American and 4690 Japanese troops. The United States government aims to identify and repatriate the remains of all missing American service members through the Defense Prisoner of War/Missing in Action (POW/MIA) Accounting Agency (DPAA) and its partners such as the Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL). Remains associated with the Battle of Tarawa have been recovered from field excavations conducted by History Flight, a DPAA strategic partner, as well as from the National Memorial Cemetery of the Pacific (NMCP) in Hawaii where unknowns have been disinterred for identification. DNA testing at the AFMES-AFDIL has produced mitochondrial DNA (mtDNA) sequences from 1027 case samples to date. Haplogroup assignments indicate that more than one third (36.2 %) of field-collected samples are likely of Asian maternal ancestry. Therefore the field collections from the Tarawa battlefield comprise the remains of American service members but also those of foreign nationals from Asia. The mtDNA of the NMCP unknowns is similar in ancestry proportion to the family reference sample distribution. The DPAA uses the ancestry information gleaned from mtDNA sequence data in conjunction with anthropological evidence to make foreign national determinations. In this way, mtDNA haplogrouping is used to sort the commingled and fragmentary remains recovered from Tarawa between Americans and foreign nationals, which are then repatriated to their country of origin.
  •  
38.
  • Montelius, Kerstin, et al. (author)
  • STR data for the AmpFlSTR Identifiler loci from Swedish population in comparison to European, as well as with non-European population
  • 2008
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 2:3, s. e49-e52
  • Journal article (peer-reviewed)abstract
    • The modern Swedish population is a mixture of people that originate from different parts of the world. This is also the truth for the clients participating in the paternity cases investigated at the department. Calculations based on a Swedish frequency database only, could give us overestimated figures of probability and power of exclusion in cases including clients with a genetic background other than Swedish. Here, we describe allele frequencies regarding the markers in the Identifiler-kit. We have compared three sets of population samples; Swedish, European and non-European to investigate how these three groups of population samples differ. Also, all three population sets were compared to data reported from other European and non-European populations.Swedish allele frequencies for the 15 autosomal STRs included in the Identifiler kit were obtained from unrelated blood donors with Swedish names. The European and non-European frequencies were based on DNA-profiles of alleged fathers from our paternity cases in 2005 and 2006.
  •  
39.
  • Nilsson, Martina, et al. (author)
  • Comparison of DNA polymerases for improved forensic analysis of challenging samples
  • 2016
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 24, s. 55-59
  • Journal article (peer-reviewed)abstract
    • Inhibitors of polymerase chain reaction (PCR) amplification often present a challenge in forensic investigations of e.g., terrorism, missing persons, sexual assaults and other criminal cases. Such inhibitors may be counteracted by dilution of the DNA extract, using different additives, and selecting an inhibitory resistant DNA polymerase. Additionally, DNA in forensic samples is often present in limited amounts and degraded, requiring special analyses of short nuclear targets or mitochondrial DNA. The present study evaluated the enzymes AmpliTaq Gold, HotStarTaq Plus, KAPA3G Plant, and KAPA2G Robust, with regard to their ability to overcome inhibitory effects. Our data showed that diluting the extracts and adding bovine serum albumin may increase the yield of the PCR product. However, the largest impact was observed when alternative enzymes were utilized, instead of the commonly used AmpliTaq Gold. KAPA2G Robust presented the highest amplification efficiency in the presence of the inhibitor ammonium nitrate. Moreover, the KAPA3G Plant enzyme had the highest efficiency in amplifying degraded DNA from old buried bone material. KAPA3G Plant and KAPA2G Robust may thus be useful for counteracting inhibitors and improving the analysis of challenging samples.
  •  
40.
  • Nilsson, Martina, et al. (author)
  • Evaluation of mitochondrial DNA coding region assays for increased discrimination in forensic analysis
  • 2008
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 2:1, s. 1-8
  • Journal article (peer-reviewed)abstract
    • There is an increasing trend to use mitochondrial DNA (mtDNA) analysis in criminal investigations where only limited amounts of DNA are available. However, analysis of the mtDNA control region has the drawback of low discrimination power, due to the lack of recombination that results from uniparental (maternal) inheritance. As a strategy to increase discrimination, a number of typing assays detecting variation in the mitochondrial coding region have been developed. In this study, several of these assays are evaluated for their discriminatory capacity using data obtained from 495 complete Caucasian mtDNA sequences. In order to add a local geographic perspective to this evaluation, we have also sequenced and analysed the entire mtDNA from 20 individuals of Swedish origin. We find that the coding region assays are very useful for resolving sequences with identical HVI/HVII regions. The best-performing coding region assay was able to discriminate 46% of the resolvable sequences, compared to 20–30% for the other coding region assays we evaluated.
  •  
41.
  • Phillips, C., et al. (author)
  • A compilation of tri-allelic SNPs from 1000 Genomes and use of the most polymorphic loci for a large-scale human identification panel
  • 2020
  • In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 46
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
42.
  •  
43.
  •  
44.
  • Sguazzi, Guilia, et al. (author)
  • Microbial DNA in human nucleic acid extracts : Recoverability of the microbiome in DNA extracts stored frozen long-term and its potential and ethical implications for forensic investigation
  • 2022
  • In: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 59, s. 1-12
  • Journal article (peer-reviewed)abstract
    • Human DNA samples can remain unaltered for years and preserve important genetic information for forensic investigations. In fact, besides human genetic information, these extracts potentially contain additional valuable information: microbiome signatures. Forensic microbiology is rapidly becoming a significant tool for estimating post-mortem interval (PMI), and establishing cause of death and personal identity. To date, the possibility to recover unaltered microbiome signatures from human DNA extracts has not been proven. This study examines the microbiome signatures within human DNA extracts obtained from six cadavers with different PMIs, which were stored frozen for 5–16 years. Results demonstrated that the microbiome can be co-extracted with human DNA using forensic kits designed to extract the human host’s DNA from different tissues and fluids during decomposition. We compared the microbial communities identified in these samples with microbial DNA recovered from two human cadavers donated to the Forensic Anthropology Center at Texas State University (FACTS) during multiple decomposition stages, to examine whether the microbial signatures recovered from “old” (up to 16 years) extracts are consistent with those identified in recently extracted microbial DNA samples. The V4 region of 16 S rRNA gene was amplified and sequenced using Illumina MiSeq for all DNA extracts. The results obtained from the human DNA extracts were compared with each other and with the microbial DNA from the FACTS samples. Overall, we found that the presence of specific microbial taxa depends on the decomposition stage, the type of tissue, and the depositional environment. We found no indications of contamination in the microbial signatures, or any alterations attributable to the long-term frozen storage of the extracts, demonstrating that older human DNA extracts are a reliable source of such microbial signatures. No shared Core Microbiome (CM) was identified amongst the total 18 samples, but we identified certain species in association with the different decomposition stages, offering potential for the use of microbial signatures co-extracted with human DNA samples for PMI estimation in future. Unveiling the new significance of older human DNA extracts brings with it important ethical-legal considerations. Currently, there are no shared legal frameworks governing the long-term storage and use of human DNA extracts obtained from crime scene evidence for additional research purposes. It is therefore important to create common protocols on the storage of biological material collected at crime scenes. We review existing legislation and guidelines, and identify some important limitations for the further development and application of forensic microbiomics.
  •  
45.
  • Sidstedt, Maja, et al. (author)
  • The impact of common PCR inhibitors on forensic MPS analysis
  • 2019
  • In: Forensic Science International: Genetics. - : Elsevier BV. - 1872-4973. ; 40, s. 182-191
  • Journal article (peer-reviewed)abstract
    • Massively parallel sequencing holds great promise for new possibilities in the field of forensic genetics, enabling simultaneous analysis of multiple markers as well as offering enhanced short tandem repeat allele resolution. A challenge in forensic DNA analysis is that the samples often contain low amounts of DNA in a background that may interfere with downstream analysis. PCR inhibition mechanisms of some relevant molecules have been studied applying e.g. real-time PCR and digital PCR. However, a detailed understanding of the effects of inhibitory molecules on forensic MPS, including mechanisms and ways to relieve inhibition, is missing. In this study, the effects of two well-characterized PCR inhibitors, humic acid and hematin, have been studied using the ForenSeq DNA Signature Prep kit. Humic acid and hematin resulted in lowered read numbers as well as specific negative effects on certain markers. Quality control of libraries with Fragment analyzer showed that increasing amounts of inhibitors caused a lowered amplicon quantity and that the larger amplicons were more likely to drop out. Further, the inhibitor tolerance could be improved 5–10 times by addition of bovine serum albumin in the initial PCR. On the contrary to the samples with inhibitors, low-template samples resulted in lowered read numbers for all markers. This difference strengthened the conclusion that the inhibitors have a negative effect on the DNA polymerase activity in the initial PCR. Additionally, a common capillary gel electrophoresis-based STR kit was shown to handle at least 200 times more inhibitors than the ForenSeq DNA Signature Prep kit. This suggests that there is room for improvement of the PCR components to ensure analytical success for challenging samples, which is needed for a broad application of MPS for forensic STR analysis.
  •  
46.
  • Sidstedt, Maja, et al. (author)
  • Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method
  • 2024
  • In: Forensic Science International: Genetics. - : Elsevier Ireland Ltd. - 1872-4973 .- 1878-0326. ; 71
  • Journal article (peer-reviewed)abstract
    • Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1–15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.
  •  
47.
  • Simonsson, Ivar, 1987, et al. (author)
  • Stationary mutation models
  • 2016
  • In: Forensic Science International-Genetics. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 23, s. 217-225
  • Journal article (peer-reviewed)abstract
    • Probability calculations for relationship inference based on DNA tests are often performed with computer packages such as Familias. When mutations are assumed to be a possibility, one may notice a curious and problematic effect of including untested parents: results tend to change slightly. In this paper, we trace this effect back to fundamental model-formulating issues which can only be resolved by using stationary mutation models. We present several methods for obtaining such stationary mutation matrices from original mutation matrices, and evaluate essential properties of these methods. Our conclusion is that typically, stationary mutation models can be obtained, but for many types of markers, it may be impossible to combine specific biologically reasonable requirements for a mutation matrix with the requirement of stationarity.
  •  
48.
  • Staadig, A., et al. (author)
  • An overall limited effect on the weight-of-evidence when taking STR DNA sequence polymorphism into account in kinship analysis
  • 2019
  • In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 39, s. 44-49
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
49.
  • Steensma, Kristy, et al. (author)
  • An inter-laboratory comparison study on transfer, persistence and recovery of DNA from cable ties
  • 2017
  • In: Forensic Science International. - : ELSEVIER IRELAND LTD. - 1872-4973 .- 1878-0326. ; 31, s. 95-104
  • Journal article (peer-reviewed)abstract
    • To address questions on the activity that led to the deposition of biological traces in a particular case, general information on the probabilities of transfer, persistence and recovery of cellular material in relevant scenarios is necessary. These figures may be derived from experimental data described in forensic literature when conditions relevant to the case were included. The experimental methodology regarding sampling, DNA extraction, DNA typing and profile interpretation that were used to generate these published data may differ from those applied in the case and thus the applicability of the literature data may be questioned. To assess the level of variability that different laboratories obtain when similar exhibits are analysed, we performed an inter-laboratory study between four partner laboratories. Five sets of 20 cable ties bound by different volunteers were distributed to the participating laboratories and sampled and processed according to the in-house protocols. Differences were found for the amount of retrieved DNA, as well as for the reportability and composition of the DNA profiles. These differences also resulted in different probabilities of transfer, persistence and recovery for each laboratory. Nevertheless, when applied to a case example, these differences resulted in similar assignments of weight of evidence given activity-level propositions.
  •  
50.
  • Strobl, Christina, et al. (author)
  • Evaluation of the precision ID whole MtDNA genome panel for forensic analyses
  • 2018
  • In: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 35, s. 21-25
  • Journal article (peer-reviewed)abstract
    • Mitochondrial DNA (mtDNA) amplification and Massively Parallel Sequencing (MPS) using an early access version of the Precision ID Whole MtDNA Genome Panel (Thermo Fisher Scientific) and the Ion Personal Genome Machine (PGM) were evaluated using 15 forensically relevant samples. Samples were selected to represent typical forensic specimens for mtDNA analysis including hairs, hair shafts, swabs and ancient solid tissue samples (bones and teeth) that were stored in the freezer for up to several years after having been typed with conventional Sanger-type Sequencing and Capillary Electrophoresis. The MPS haplotypes confirmed the earlier results in all samples and provided additional sequence information that improved discrimination power and haplogroup estimation. The results raised the appetite for further experiments to validate and apply the new technology in forensic practice.
  •  
Skapa referenser, mejla, bekava och länka
  • Result 1-50 of 66
Type of publication
journal article (64)
research review (2)
Type of content
peer-reviewed (62)
other academic/artistic (4)
Author/Editor
Ansell, Ricky (14)
Hedman, Johannes (13)
Tillmar, Andreas (13)
Allen, Marie (10)
Kling, Daniel (9)
Jansson, Linda (7)
show more...
Parson, Walther (6)
Mostad, Petter, 1964 (5)
Forsberg, Christina (5)
Egeland, Thore (5)
Green, Henrik (4)
Hedell, Ronny (4)
Holmlund, Gunilla (4)
Marshall, Charla (4)
Connolly, Edward (4)
Kokshoorn, Bas (4)
Sturk-Andreaggi, Kim ... (4)
Montelius, Kerstin (4)
Tillmar, Andreas O. (4)
Kloosterman, Ate D. (4)
McKenna, Louise G. (4)
Szkuta, Bianca (4)
Lindblom, Bertil (3)
Nilsson, Martina (3)
Boiso, Lina (3)
Sidstedt, Maja (3)
Bus, Magdalena M. (3)
Kiesler, Kevin M. (3)
Vallone, Peter M. (3)
Akel, Yasmine (3)
Phillips, C. (2)
Albinsson, Linda (2)
Norén, Lina (2)
Edlund, Hanna (2)
Jakobsson, Mattias (2)
Nilsson, Helena (2)
Rådström, Peter (2)
Ansell, Ricky, 1967- (2)
Sijen, Titia (2)
Prainsack, Barbara (2)
Strobl, Christina (2)
McMahon, Timothy P. (2)
Clarisse, Lindy (2)
Schneider, Peter M. (2)
Wallmark, Nanny (2)
Ansell, Carina (2)
Gorden, Erin M. (2)
de la Puente, M. (2)
Bastisch, I. (2)
Parson, W. (2)
show less...
University
Linköping University (38)
Uppsala University (18)
Lund University (14)
University of Gothenburg (5)
Chalmers University of Technology (5)
Umeå University (1)
show more...
Stockholm University (1)
University West (1)
Örebro University (1)
Linnaeus University (1)
RISE (1)
Karolinska Institutet (1)
show less...
Language
English (66)
Research subject (UKÄ/SCB)
Medical and Health Sciences (30)
Natural sciences (29)
Engineering and Technology (4)
Social Sciences (2)
Humanities (2)

Year

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Close

Copy and save the link in order to return to this view