| 1. |
- Shrine, Nick, et al.
(författare)
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New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries
- 2019
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 51:3, s. 481-493
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Tidskriftsartikel (refereegranskat)abstract
- Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent populations. Furthermore, the combined effect of these variants showed generalizability across smokers and never smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function-associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD.
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| 2. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 3. |
- Fuhlbrigge, Anne L., et al.
(författare)
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A novel endpoint for exacerbations in asthma to accelerate clinical development : A post-hoc analysis of randomised controlled trials
- 2017
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Ingår i: The Lancet Respiratory Medicine. - 2213-2600. ; 5:7, s. 577-590
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Tidskriftsartikel (refereegranskat)abstract
- Background: Occurrence of severe asthma exacerbations are the cornerstone of the evaluation of asthma management, but severe asthma exacerbations are rare events. Therefore, trials that assess drug efficacy on exacerbations are done late in clinical development programmes. We aimed to establish an endpoint capturing clinically relevant deteriorations (diary events) that, when combined with severe exacerbations, create a composite outcome (CompEx). CompEx needs to strongly mirror results seen with the severe exacerbation-validated outcome, to allow the design of clinical trials of shorter duration and that include fewer patients than trials assessing severe exacerbations. Methods: Data from 12 asthma trials of 6 months or 12 months duration and, with standardised collection of exacerbations and diary card variables, were used to construct and test CompEx. The study populations had a mean age of 35-53 years, 59-69% were female, and had a mean FEV1 percentage of predicted normal of 63-84%. With data from five trials, we established a series of diary events based on peak expiratory flow (P), reliever use (R), symptoms (S), awakenings (A), and threshold values for change from baseline and slopes to assess trends. For the development phase, we evaluated different variable combinations and deterioration criteria to select the most robust algorithm to define a diary event for the composite outcome. We defined a composite outcome, CompEx, as first occurrence of a diary event or a severe exacerbation. We assessed the performance of CompEx in seven trials by comparing the event frequency, treatment effect (hazard ratio; HR), and the sample size needed for future trials for the CompEx versus episodes of severe exacerbations. Findings: CompEx (based on PRS) was the algorithm that best fulfilled our two-set criteria. When censored at 3 months, CompEx resulted in 2·8 times more events than severe exacerbations, and while preserving the treatment effect observed on severe exacerbations (CompEx over severe exacerbation average HR 1·01). The increased number of events, together with the sustained treatment effect, resulted in a large net gain in power, with a 67% mean reduction in the number of patients required in a drug trial for severe exacerbations. In six of seven comparisons tested, CompEx reduced the sample size needed by at least 50%. Validation of independent test populations confirmed the ability of CompEx to increase event frequencies, preserve treatment effect, and reduce the number of patients needed. Interpretation: CompEx is a composite outcome for evaluation of new asthma therapies. CompEx allows design of shorter trials that require fewer patients than studies of severe exacerbations, while preserving the ability to show a treatment effect compared with severe exacerbations. Funding: AstraZeneca.
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| 6. |
- Roberts, Sean, et al.
(författare)
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CHIELD: the causal hypotheses in evolutionary linguistics database
- 2020
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Ingår i: Journal of Language Evolution. - : Oxford University Press (OUP). - 2058-458X. ; 5:2, s. 101-120
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Tidskriftsartikel (refereegranskat)abstract
- Language is one of the most complex of human traits. There are many hypotheses about how it originated, what factors shaped its diversity, and what ongoing processes drive how it changes. We present the Causal Hypotheses in Evolutionary Linguistics Database (CHIELD, https://chield.excd.org/), a tool for expressing, exploring, and evaluating hypotheses. It allows researchers to integrate multiple theories into a coherent narrative, helping to design future research. We present design goals, a formal specification, and an implementation for this database. Source code is freely available for other fields to take advantage of this tool. Some initial results are presented, including identifying conflicts in theories about gossip and ritual, comparing hypotheses relating population size and morphological complexity, and an author relation network.
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| 7. |
- Sakornsakolpat, Phuwanat, et al.
(författare)
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Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
- 2019
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 51:3, s. 494-505
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Tidskriftsartikel (refereegranskat)abstract
- Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P < 5 x 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
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| 8. |
- Schmid Neset, Tina, et al.
(författare)
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Understanding consumption-related sucralose emissions - A conceptual approach combining substance-flow analysis with sampling analysis
- 2010
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Ingår i: Science of the Total Environment. - : Elsevier Science B.V., Amsterdam.. - 0048-9697 .- 1879-1026. ; 408:16, s. 3261-3269
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Tidskriftsartikel (refereegranskat)abstract
- This paper explores the potential of combining substance-flow modelling with water and wastewater sampling to trace consumption-related substances emitted through the urban wastewater. The method is exemplified on sucralose. Sucralose is a chemical sweetener that is 600 times sweeter than sucrose and has been on the European market since 2004. As a food additive, sucralose has recently increased in usage in a number of foods, such as soft drinks, dairy products, candy and several dietary products. In a field campaign, sucralose concentrations were measured in the inflow and outflow of the local wastewater treatment plant in Linkoping, Sweden, as well as upstream and downstream of the receiving stream and in Lake Roxen. This allows the loads emitted from the city to be estimated. A method consisting of solid-phase extraction followed by liquid chromatography and high resolution mass spectrometry was used to quantify the sucralose in the collected surface and wastewater samples. To identify and quantify the sucralose sources, a consumption analysis of households including small business enterprises was conducted as well as an estimation of the emissions from the local food industry. The application of a simple model including uncertainty and sensitivity analysis indicates that at present not one large source but rather several small sources contribute to the load coming from households, small business enterprises and industry. This is in contrast to the consumption pattern seen two years earlier, which was dominated by one product. The inflow to the wastewater treatment plant decreased significantly from other measurements made two years earlier. The study shows that the combination of substance-flow modelling with the analysis of the loads to the receiving waters helps us to understand consumption-related emissions.
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| 10. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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