| 1. |
- Franceschini, N., et al.
(författare)
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GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Carotid artery intima media thickness (cIMT) and carotid plaque are measures of subclinical atherosclerosis associated with ischemic stroke and coronary heart disease (CHD). Here, we undertake meta-analyses of genome-wide association studies (GWAS) in 71,128 individuals for cIMT, and 48,434 individuals for carotid plaque traits. We identify eight novel susceptibility loci for cIMT, one independent association at the previously-identified PINX1 locus, and one novel locus for carotid plaque. Colocalization analysis with nearby vascular expression quantitative loci (cis-eQTLs) derived from arterial wall and metabolic tissues obtained from patients with CHD identifies candidate genes at two potentially additional loci, ADAMTS9 and LOXL4. LD score regression reveals significant genetic correlations between cIMT and plaque traits, and both cIMT and plaque with CHD, any stroke subtype and ischemic stroke. Our study provides insights into genes and tissue-specific regulatory mechanisms linking atherosclerosis both to its functional genomic origins and its clinical consequences in humans. © 2018, The Author(s).
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| 2. |
- Ramdas, S., et al.
(författare)
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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
- 2022
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Ingår i: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 109:8, s. 1366-1387
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Tidskriftsartikel (refereegranskat)abstract
- A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
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| 3. |
- Clifton, N.E., et al.
(författare)
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Schizophrenia copy number variants and associative learning
- 2017
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Ingår i: Molecular Psychiatry. - : Springer Science and Business Media LLC. - 1359-4184 .- 1476-5578. ; 22, s. 178-182
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Tidskriftsartikel (refereegranskat)abstract
- Large-scale genomic studies have made major progress in identifying genetic risk variants for schizophrenia. A key finding from these studies is that there is an increased burden of genomic copy number variants (CNVs) in schizophrenia cases compared with controls. The mechanism through which these CNVs confer risk for the symptoms of schizophrenia, however, remains unclear. One possibility is that schizophrenia risk CNVs impact basic associative learning processes, abnormalities of which have long been associated with the disorder. To investigate whether genes in schizophrenia CNVs impact on specific phases of associative learning we combined human genetics with experimental gene expression studies in animals. In a sample of 11 917 schizophrenia cases and 16 416 controls, we investigated whether CNVs from patients with schizophrenia are enriched for genes expressed during the consolidation, retrieval or extinction of associative memories. We show that CNVs from cases are enriched for genes expressed during fear extinction in the hippocampus, but not genes expressed following consolidation or retrieval. These results suggest that CNVs act to impair inhibitory learning in schizophrenia, potentially contributing to the development of core symptoms of the disorder.
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| 4. |
- Davies, G., et al.
(författare)
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Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function
- 2018
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- General cognitive function is a prominent and relatively stable human trait that is associated with many important life outcomes. We combine cognitive and genetic data from the CHARGE and COGENT consortia, and UK Biobank (total N = 300,486; age 16-102) and find 148 genome-wide significant independent loci (P < 5 × 10-8) associated with general cognitive function. Within the novel genetic loci are variants associated with neurodegenerative and neurodevelopmental disorders, physical and psychiatric illnesses, and brain structure. Gene-based analyses find 709 genes associated with general cognitive function. Expression levels across the cortex are associated with general cognitive function. Using polygenic scores, up to 4.3% of variance in general cognitive function is predicted in independent samples. We detect significant genetic overlap between general cognitive function, reaction time, and many health variables including eyesight, hypertension, and longevity. In conclusion we identify novel genetic loci and pathways contributing to the heritability of general cognitive function.
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| 5. |
- Ford, J.S., et al.
(författare)
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Proposed Local Ecological Impact Categories and Indicators for Life Cycle Assessment of Aquaculture : A Salmon Aquaculture Case Study
- 2012
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Ingår i: Journal of Industrial Ecology. - : Wiley. - 1088-1980 .- 1530-9290. ; 16:2, s. 254-265
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Tidskriftsartikel (refereegranskat)abstract
- In this study we discuss impact categories and indicators to incorporate local ecological impacts into life cycle assessment (LCA) for aquaculture. We focus on the production stages of salmon farming-freshwater hatcheries used to produce smolts and marine grow-out sites using open netpens. Specifically, we propose two impact categories: impacts of nutrient release and impacts on biodiversity. Proposed indicators for impacts of nutrient release are (1) the area altered by farm waste, (2) changes in nutrient concentration in the water column, (3) the percent of carrying capacity reached, (4) the percent of total anthropogenic nutrient release, and (5) release of wastes into freshwater. Proposed indicators for impacts on biodiversity are (1) the number of escaped salmon, (2) the number of reported disease outbreaks, (3) parasite abundance on farms, and (4) the percent reduction in wild salmon survival. For each proposed indicator, an example of how the indicator could be estimated is given and the strengths and weaknesses of that indicator are discussed. We propose that including local environmental impacts as well as global-scale ones in LCA allows us to better identify potential trade-offs, where actions that are beneficial at one scale are harmful at another, and synchronicities, where actions have desirable or undesirable effects at both spatial scales. We also discuss the potential applicability of meta-analytic statistical techniques to LCA. © 2012 by Yale University.
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| 6. |
- Kruse, S.A., et al.
(författare)
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Socioeconomic indicators as a complement to life cycle assessment : An application to salmon production systems
- 2009
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Ingår i: The International Journal of Life Cycle Assessment. - : Springer Science and Business Media LLC. - 0948-3349 .- 1614-7502. ; 14:1, s. 42234-
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Tidskriftsartikel (refereegranskat)abstract
- Background, aim, and scope: There is a growing recognition on the part of industry, policymakers, and consumers that sustainable industry practices are needed to maintain environmental and social well being. Life cycle assessment (LCA) is an internationally standardized analytical framework that has traditionally focused on evaluation of the environmental impacts of processes or products using a cradle-to-grave approach. Yet, sustainability, defined generally, requires that assessments consider not only environmental but also social and economic impacts-the other two pillars of sustainability. Even though the LCA methodology has the potential to include both social and economic indicators, and SETAC guidelines recommend the inclusion of such impact categories in all detailed LCAs, no established set of metrics exists to describe the relationship between socioeconomic indicators (SEIs) and a specific product or process; nor is there a common understanding on how such metrics might be developed. This article presents the methods for and development of a suite of socioeconomic indicators that complement the LCA methodology and provides a comprehensive approach for assessing the cradle-to-grave sustainability of a product or process. Methods: A combined top-down and bottom-up approach serves as the basis for development of the set of socioeconomic indicators presented here. Generally recognized societal values, industry specific issues, and financial constraints associated with collection of data necessary for measurement of the indicators are all factors considered in this approach. In our categorization, socioeconomic indicators fall into two types: additive indicators and descriptive indicators. Results: Indicators are categorized based on fundamental methodological differences and then used to describe the socioeconomic impacts associated with salmon production. Additive indicators (e.g., production costs and value added) and descriptive indicators (e.g., fair wage and contribution to personal income) are both discussed. Discussion: There is a need to further develop and refine methods to assess the results of socioeconomic indicators using a life cycle perspective. It would be most interesting to conduct additional case studies that focus on such methodological development, particularly trade-offs between stakeholder groups and pillars of sustainability. Additional areas of discussion are (1) the need for data to populate socioeconomic indicators and (2) defining system boundaries for socioeconomic indicators. Conclusions: This article presents a set of socioeconomic indicators designed to serve as a complement for the LCA framework, thus, increasing the framework's effectiveness as a measure of the overall sustainability of a product or process. Development of socioeconomic indicators as a complement to LCA is still in its early stages, however, and further research is required. Recommendations and perspectives: The SEIs presented here are discussed theoretically within the context of salmon food production systems, but a test of the practicability and validity of the indicators (i.e., a practical application) is also necessary. The practical application of the topic will be presented in a forthcoming paper. © 2008 Springer-Verlag.
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| 7. |
- Legradi, J. B., et al.
(författare)
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An ecotoxicological view on neurotoxicity assessment
- 2018
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Ingår i: Environmental Sciences Europe. - : Springer. - 2190-4707 .- 2190-4715. ; 30
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Forskningsöversikt (refereegranskat)abstract
- The numbers of potential neurotoxicants in the environment are raising and pose a great risk for humans and the environment. Currently neurotoxicity assessment is mostly performed to predict and prevent harm to human populations. Despite all the efforts invested in the last years in developing novel in vitro or in silico test systems, in vivo tests with rodents are still the only accepted test for neurotoxicity risk assessment in Europe. Despite an increasing number of reports of species showing altered behaviour, neurotoxicity assessment for species in the environment is not required and therefore mostly not performed. Considering the increasing numbers of environmental contaminants with potential neurotoxic potential, eco-neurotoxicity should be also considered in risk assessment. In order to do so novel test systems are needed that can cope with species differences within ecosystems. In the field, online-biomonitoring systems using behavioural information could be used to detect neurotoxic effects and effect-directed analyses could be applied to identify the neurotoxicants causing the effect. Additionally, toxic pressure calculations in combination with mixture modelling could use environmental chemical monitoring data to predict adverse effects and prioritize pollutants for laboratory testing. Cheminformatics based on computational toxicological data from in vitro and in vivo studies could help to identify potential neurotoxicants. An array of in vitro assays covering different modes of action could be applied to screen compounds for neurotoxicity. The selection of in vitro assays could be guided by AOPs relevant for eco-neurotoxicity. In order to be able to perform risk assessment for eco-neurotoxicity, methods need to focus on the most sensitive species in an ecosystem. A test battery using species from different trophic levels might be the best approach. To implement eco-neurotoxicity assessment into European risk assessment, cheminformatics and in vitro screening tests could be used as first approach to identify eco-neurotoxic pollutants. In a second step, a small species test battery could be applied to assess the risks of ecosystems.
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| 8. |
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Overview of the JET results
- 2015
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 55:10
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Tidskriftsartikel (refereegranskat)
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| 9. |
- Zewinger, Stephen, et al.
(författare)
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Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease : a molecular and genetic association study
- 2017
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Ingår i: The Lancet Diabetes and Endocrinology. - : ELSEVIER SCIENCE INC. - 2213-8587 .- 2213-8595. ; 5:7, s. 534-543
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Tidskriftsartikel (refereegranskat)abstract
- Background: Lipoprotein(a) concentrations in plasma are associated with cardiovascular risk in the general population. Whether lipoprotein(a) concentrations or LPA genetic variants predict long-term mortality in patients with established coronary heart disease remains less clear.Methods: We obtained data from 3313 patients with established coronary heart disease in the Ludwigshafen Risk and Cardiovascular Health (LURIC) study. We tested associations of tertiles of lipoprotein(a) concentration in plasma and two LPA single-nucleotide polymorphisms ([SNPs] rs10455872 and rs3798220) with all-cause mortality and cardiovascular mortality by Cox regression analysis and with severity of disease by generalised linear modelling, with and without adjustment for age, sex, diabetes diagnosis, systolic blood pressure, BMI, smoking status, estimated glomerular filtration rate, LDL-cholesterol concentration, and use of lipid-lowering therapy. Results for plasma lipoprotein(a) concentrations were validated in five independent studies involving 10 195 patients with established coronary heart disease. Results for genetic associations were replicated through large-scale collaborative analysis in the GENIUS-CHD consortium, comprising 106 353 patients with established coronary heart disease and 19 332 deaths in 22 studies or cohorts.Findings: The median follow-up was 9.9 years. Increased severity of coronary heart disease was associated with lipoprotein(a) concentrations in plasma in the highest tertile (adjusted hazard radio [HR] 1.44, 95% CI 1.14-1.83) and the presence of either LPA SNP (1.88, 1.40-2.53). No associations were found in LURIC with all-cause mortality (highest tertile of lipoprotein(a) concentration in plasma 0.95, 0.81-1.11 and either LPA SNP 1.10, 0.92-1.31) or cardiovascular mortality (0.99, 0.81-1.2 and 1.13, 0.90-1.40, respectively) or in the validation studies.Interpretation: In patients with prevalent coronary heart disease, lipoprotein(a) concentrations and genetic variants showed no associations with mortality. We conclude that these variables are not useful risk factors to measure to predict progression to death after coronary heart disease is established.
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