Structural variants (SVs) are physical changes in the structure of chromosomes and include both unbalanced copy number variants (CNVs) and balanced events (translocations, inversions and insertions). ...Many SVs constitute benign background variation and are found frequently in healthy individuals. Others may cause disease through gene disruption, deletion or duplication of dosage sensitive genes, or by disrupting the 3D structure of the genome.In this thesis, we have delineated the exact structure of rearranged chromosomes and performed breakpoint junction analysis to study mutational signatures and underlying mechanisms of formation.In paper I, we characterized and analyzed breakpoint junction sequences of 23cytogenetically balanced translocations with mate-pair whole genome sequencing (WGS) and17% of the translocations had microhomology and/or templated insertions in the breakpoint junctions, indicative of replication-based repair mechanisms. Genes were disrupted in 48% of breakpoints, highlighting a number of novel candidate genes and providing a molecular diagnosis in three cases. In paper II, we used targeted array comparative genomic hybridization and WGS to show that intragenic exonic duplications, formed through Alu-Alu fusion events, within MATN3 and IFT81 cause monogenic skeletal dysplasia disorders. Follow-up studies in primary cells and in zebrafish embryos showed that expression of a shorter IFT81 transcript alone is compatible with life. In paper III, we used WGS to investigate a benign complex chromosome rearrangement on chromosome 5p, detected in a healthy woman, which through unequal crossing-over during meiosis evolved into a pathogenic rearrangement including a duplication of the NIPBL gene in her daughter. In paper IV, we characterized the breakpoint junctions in 16 cytogenetically . Contrary to what was expected, the vast majority of the resolved inversions were not mediated by inverted repeats through non-allelic homologous recombination. The mutational signatures in all the resolved inversions (11/16) indicate other mechanisms than ectopic recombination including replicative mechanisms in 2 cases. In paper V, we utilized WGS to perform a detailed characterization of 21 cases harboring multiple CNVs clustering on the same chromosome. The analysis revealed that multiple cellular mechanisms are involved in the formation of such SVs.In conclusion, the results of this thesis show that WGS is a powerful way to delineate the structure of balanced, unbalanced and complex SVs. These studies have identified disease causing aberrations, new candidate genes for further studies of neurodevelopmental disorders, and contributed to the understanding of how, when and why SVs arise.
Cytogenetically detected inversions are generally assumed to be copy number and phenotypically neutral events. While nonallelic homologous recombination is thought to play a major role, recent data ...suggest the involvement of other molecular mechanisms in inversion formation. Using a combination of short‐read whole‐genome sequencing (WGS), 10X Genomics Chromium WGS, droplet digital polymerase chain reaction and array comparative genomic hybridization we investigated the genomic structure of 18 large unique cytogenetically detected chromosomal inversions and achieved nucleotide resolution of at least one chromosomal inversion junction for 13/18 (72%). Surprisingly, we observed that seemingly copy number neutral inversions can be accompanied by a copy‐number gain of up to 350 kb and local genomic complexities (3/18, 17%). In the resolved inversions, the mutational signatures are consistent with nonhomologous end‐joining (8/13, 62%) or microhomology‐mediated break‐induced replication (5/13, 38%). Our study indicates that short‐read 30x coverage WGS can detect a substantial fraction of chromosomal inversions. Moreover, replication‐based mechanisms are responsible for approximately 38% of those events leading to a significant proportion of inversions that are actually accompanied by additional copy‐number variation potentially contributing to the overall phenotypic presentation of those patients.
This study indicates that short‐read whole‐genome sequencing can detect a substantial fraction of cytogenetically visible chromosomal inversions. In addition, replication‐based mechanisms are responsible for approximately 38% of those events, leading to a significant proportion of inversions that are actually accompanied by additional copy‐number variation potentially contributing to the overall phenotypic presentation of those patients.
Background
Autoimmune Addison's disease (AAD) is the most common cause of primary adrenal insufficiency (PAI). Despite its exceptionally high heritability, tools to estimate disease susceptibility in ...individual patients are lacking. We hypothesized that polygenic risk score (PRS) for AAD could help investigate PAI pathogenesis in pediatric patients.
Methods
We here constructed and evaluated a PRS for AAD in 1223 seropositive cases and 4097 controls. To test its clinical utility, we reevaluated 18 pediatric patients, whose whole genome we also sequenced. We next explored the individual PRS in more than 120 seronegative patients with idiopathic PAI.
Results
The genetic susceptibility to AAD—quantified using PRS—was on average 1.5 standard deviations (SD) higher in patients compared with healthy controls (p < 2e − 16), and 1.2 SD higher in the young patients compared with the old (p = 3e − 4). Using the novel PRS, we searched for pediatric patients with strikingly low AAD susceptibility and identified cases of monogenic PAI, previously misdiagnosed as AAD. By stratifying seronegative adult patients by autoimmune comorbidities and disease duration we could delineate subgroups of PRS suggesting various disease etiologies.
Conclusions
The PRS performed well for case‐control differentiation and susceptibility estimation in individual patients. Remarkably, a PRS for AAD holds promise as a means to detect disease etiologies other than autoimmunity.
This study reviews how the issue of ash dieback has been placed on the political agenda in the UK, a country where the disease has affected one of the largest national extents, thus representing a ...particularly severe case. Comparisons are made between how the scientific community framed the ash dieback threat and the resulting response strategy and how both the media and the British government framed the problem. Representing one example of media framing, the study analyses one British newspaper’s coverage of the disease and the response strategies (the Daily Telegraph). The analysis highlights a gap between the biologically rooted perspective and the perspective of policymakers, where policy must manoeuvre between disparate viewpoints and needs. Crucially, none of Pautasso et al.’s (Biol Conserv 158:37–49,
2013
) five plant-science-based solutions were explicitly adopted by the British Government in their response strategy to ash dieback disease. The same is true of the biological control recommendations offered by Kirisits et al. (J Agric Ext Rural Dev 4(9):230–235,
2012
). Instead, the government adopted a broader, more comprehensive approach than that recommended by plant scientists. The present analysis thus provides an example of a holistic perspective on the multiple competing factors that policymakers must navigate in their attempts to delineate action. It highlights instances in which proposed biological responses were rendered less applicable by a failure to understand the agenda-setting process and the policy-making arena. The present findings suggest that an improved understanding of the factors influencing agenda setting and policy action is essential to arriving at a more effective and integrated understanding of responses to biological threats.
Northern Europe is often seen as having a specific relation to nature. In this manuscript, the policy and regulatory frameworks in Norway and Sweden are compared when it comes to the scope for local ...use that is provided by the regulatory frameworks relating to natural resources. The paper analyzes the legal framework for the use of nature and its resources, including hunting, fishing, and reindeer husbandry, with a focus on the Swedish natural resource legislation in relation to the (corresponding) Norwegian Finnmark Act. The study thereby compares the Finnmark Act and the protection it affords local resource users with that in northern Sweden under general Swedish and municipal regulatory systems.
This article explores and analyzes the nexus between climate change, environmental threats, and cyber-threats in a multi-regulatory contextual sustainable global approach with Sweden as an example. ...Research and collection of material have been conducted with the precise aim to draw a parallel between environmental regulations and the cyberspace and cybersecurity systems. Many aspects of the cyber-security system are not known and are highly fragmented. Selected points of the study of the Swedish cyber strategy are being developed in parallel to the environmental regime in order to better understand how to improve the effectiveness of the cyber complex regime from a contextual perspective. One way to better understand the cybersecurity system is to make an interdisciplinary study of how best to coordinate these systems, thus making both cyber law and policy more effective. This leads to bringing evidence on how to take inspiration from a regime system (environmental law or, more concretely, the environmental liability framework) and using it as source of inspiration to understand and shape the formation of another system in another area, namely cybersecurity. The method of this ongoing research consists of choosing and applying key aspects of environmental law (such as concepts and principles) and comparing them with comparable selected cybersecurity key aspects, which are selected because they present strong similarities with their “equivalent” focal points pertaining to the environmental system. When conducting this comparison, multi-level governance is applied too, which means analysis of the sources of law and policy existing at Global/Regional/National (local) levels in order to understand the interactions between different levels. The analytical task of the research consists of choosing some focal points from the environmental liability system that are very similar and comparable to those of the cyber regime.
Skeletal dysplasias are a diverse group of rare Mendelian disorders with clinical and genetic heterogeneity. Here, we used targeted copy number variant (CNV) screening and identified intragenic ...exonic duplications, formed through Alu‐Alu fusion events, in two individuals with skeletal dysplasia and negative exome sequencing results. First, we detected a homozygous tandem duplication of exon 9 and 10 in IFT81 in a boy with Jeune syndrome, or short‐rib thoracic dysplasia (SRTD) (MIM# 208500). Western blot analysis did not detect any wild‐type IFT81 protein in fibroblasts from the patient with the IFT81 duplication, but only a shorter isoform of IFT81 that was also present in the normal control samples. Complementary zebrafish studies suggested that loss of full‐length IFT81 protein but expression of a shorter form of IFT81 protein affects the phenotype while being compatible with life. Second, a de novo tandem duplication of exons 2 to 5 in MATN3 was identified in a girl with multiple epiphyseal dysplasia (MED) type 5 (MIM# 607078). Our data highlights the importance of detection and careful characterization of intragenic duplication CNVs, presenting them as a novel and very rare genetic mechanism in IFT81‐related Jeune syndrome and MATN3‐related MED.
We used targeted array and WGS to detect and characterize Alu‐Alu mediated intragenic duplications in two individuals with distinct skeletal dysplasias, Jeune syndrome and multiple epiphyseal dysplasia (MED) type 5. The homozygous IFT81 duplication was inherited from heterozygous, unaffected parents and the heterozygous MATN3 duplication had arisen de novo. Studies in primary cells and zebrafish showed that the IFT81 duplication results in loss of a specific splice isoform, highlighting the importance of transcript‐specific mutations in the pathogenesis of rare diseases.
Industrial pollution accounts for a large proportion of global pollution, and in the European Union, an integrated pollution and prevention approach based on individual performance standards has been ...implemented to regulate emissions from industrial plants. Crucial for the assessment of the licensing conditions are the Best Available Technique (BAT) requirements, which should be set in accordance with the recently introduced Industrial Emissions Directive (IED). In this paper, we review and assess the licensing of industrial plants in one of the Member States, namely Sweden. Specifically, we discuss how the existing regulations (including the IED) manage to address potential trade-offs between important regulatory design issues, such as flexibility, predictability and the need to provide continuous incentives for environmental improvements. The analysis indicates that while the EU regulations provide flexibility in terms of the choice of compliance measures, in Sweden, it enters an existing regulatory framework that adds a lot of uncertainty with respect to the outcome of the licensing processes. An important challenge for the implementation of the IED is to implement performance standards that lead to continuous incentives to improve environmental performance in industrial sectors without, at the same time, adding new uncertainties. While standards ideally should be both flexible and predictable, achieving one of these criteria may often come at the expense of the other.
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