| 1. |
- Gorden, Erin M., et al.
(författare)
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Extended kinship analysis of historical remains using SNP capture
- 2022
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 57
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Tidskriftsartikel (refereegranskat)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.
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| 2. |
- Cavagnino, Courtney, et al.
(författare)
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Unearthing who and Y at Harewood Cemetery and inference of George Washington's Y-chromosomal haplotype
- 2024
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Ingår i: iScience. - : CELL PRESS. - 2589-0042. ; 27:4
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Tidskriftsartikel (refereegranskat)abstract
- An excavation conducted at Harewood Cemetery to identify the unmarked grave of Samuel Washington resulted in the discovery of burials presumably belonging to George Washington's paternal grandnephews and their mother, Lucy Payne. To confirm their identities this study examined Y -chromosomal, mitochondrial, and autosomal DNA from the burials and a living Washington descendant. The burial's Y-STR profile was compared to FamilyTreeDNA's database, which resulted in a one-step difference from the living descendant and an exact match to another Washington. A more complete Y-STR and Y -SNP profile from the descendant was inferred to be the Washington Y profile. Kinship comparisons performed in relation to the descendant, who is a 4 th and 5 th degree relative of the putative individuals, resulted in >37,000 overlapping autosomal SNPs and strong statistical support with likelihood ratios exceeding one billion. This study highlights the benefits of a multi -marker approach for kinship prediction and DNA -assisted identification of historical remains.
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| 3. |
- Gorden, Erin M., et al.
(författare)
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Capture enrichment and massively parallel sequencing for human identification
- 2021
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Ingår i: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 53
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Forskningsöversikt (refereegranskat)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.
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| 4. |
- Hoppe, Magnus, 1963-, et al.
(författare)
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Intended Involvement – How Public Organizations Struggle to Become Co-producers of New Public Values
- 2024
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Ingår i: Scandinavian Journal of Public Administration. - : University of Gothenburg School of Public Administration. - 2001-7405 .- 2001-7413. ; 28:1, s. 78-98
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Tidskriftsartikel (refereegranskat)abstract
- The paper is guided by the question of how public organizations can adapt to include citizens as co-producers of public values. To answer it, eleven researchers and civil servants, all involved in the transformation of a collaborative platform encompassing a university and four different public organizations, formed a collaborative and boundary-spanning author. Building on personal expertise and situated organizational experiences we conclude that public organizations do not adapt except for specific confined areas where they can still control and command outcomes important to them. Hence, public organizations struggle to become co-producers of new public values. From the process, we also conclude that academics and civil servants together writing an academic article cannot be viewed as a fertile common ground for equal collaboration and co-production. Nevertheless, it might still work as an interesting boundary-spanning activity for arriving at shared understandings and important insights on for instance why organizational moves from intended to actual involvement appear difficult.
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| 5. |
- Malehmir, Alireza, 1977-, et al.
(författare)
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High-resolution Seismic Investigations of a Geological Energy-storage Site - Dalby (Tornquist Zone), Southwest Sweden
- 2017
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Konferensbidrag (refereegranskat)abstract
- Three high-resolution refraction and reflection seismic profiles for the planning of a major underground thermal-energy-storage site within the Tornquist suture zone of Scania in southwest of Sweden were acquired during August 2015. Combined cabled- and wireless recorders were used to provide continuity on both side of a major road running in the middle of the study area. First arrivals are clear in most shot gathers allowing them to be used for traditional refraction seismic data analysis and also for more advanced traveltime tomography. Bedrock depressions are clearly observed in the tomograms suggesting the possibility of weakness zones, highly fractured and/or weathered, in the bedrock and confirmed in several places by boreholes. Signs of reflections in raw shot gathers were encouraging and motivated to process the reflection component of the data. Several steeply-dipping reflections were imaged down to 400 m depth. The origins of the reflections are unclear right now ranging from amphibolite sheets to diabase dykes as well as faults within the gneissic rocks, and each of this implies a different geological scenario at where the site will be developed. This study however illustrates the potential of the combined refraction and reflection imaging for underground energy-storage-site characterizations.
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| 6. |
- Sturk, Christopher, et al.
(författare)
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Tuning a synthetic in vitro oscillator using control-theoretic tools
- 2010
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Ingår i: Proceedings of the IEEE Conference on Decision and Control. - NEW YORK : IEEE. - 9781424477463 ; , s. 2554-2559
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- This paper demonstrates the effectiveness of simple control-theoretic tools in generating simulation-guided experiments on a synthetic in vitro oscillator. A theoretical analysis of the behavior of such system is motivated by high cost, time consuming experiments, together with the excessive number of tuning parameters. A simplified model of the synthetic oscillator is chosen to capture only its essential features. The model is analyzed using the small gain theorem and the theory of describing functions. Such analysis reveals what are the parameters that primarily determine when the system can admit stable oscillations. Experimental verification of the theoretical and numerical findings is carried out and confirms the predicted results regarding the role of production and degradation rates.
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