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2.
  • Birney, Ewan, et al. (författare)
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
  • 2007
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
  • 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.
  • Clark, Andrew G., et al. (författare)
  • Evolution of genes and genomes on the Drosophila phylogeny.
  • 2007
  • Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
  • Tidskriftsartikel (refereegranskat)abstract
    • Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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4.
  • Naehrlich, L., et al. (författare)
  • Incidence of SARS-CoV-2 in people with cystic fibrosis in Europe between February and June 2020
  • 2021
  • Ingår i: Journal of Cystic Fibrosis. - 1569-1993. ; 20:4, s. 566-577
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Viral infections can cause significant morbidity in cystic fibrosis (CF). The current Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic could therefore have a serious impact on the health of people with CF (pwCF). Methods: We used the 38-country European Cystic Fibrosis Society Patient Registry (ECFSPR) to collect case data about pwCF and SARS-CoV-2 infection. Results: Up to 30 June 2020, 16 countries reported 130 SARS-CoV-2 cases in people with CF, yielding an incidence of 2.70/10 0 0 pwCF. Incidence was higher in lung-transplanted patients (n = 23) versus non transplanted patients (n = 107) (8.43 versus 2.36 cases/10 0 0). Incidence was higher in pwCF versus the age-matched general population in the age groups < 15, 15-24, and 25-49 years (p < 0.001), with similar trends for pwCF with and without lung transplant. Compared to the general population, pwCF (regardless of transplantation status) had significantly higher rates of admission to hospital for all age groups with available data, and higher rates of intensive care, although not statistically significant. Most pwCF recovered (96.2%), however 5 died, of whom 3 were lung transplant recipients. The case fatality rate for pwCF (3.85%, 95% CI: 1.26-8.75) was non-significantly lower than that of the general population (7.46%; p = 0.133). Conclusions: SARS-CoV-2 infection can result in severe illness and death for pwCF, even for younger patients and especially for lung transplant recipients. PwCF should continue to shield from infection and should be prioritized for vaccination. (c) 2021 The Authors. Published by Elsevier B.V. on behalf of European Cystic Fibrosis Society. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )
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5.
  • Simard, Julia F., et al. (författare)
  • Ten years with biologics : to whom do data on effectiveness and safety apply?
  • 2011
  • Ingår i: Rheumatology. - : Oxford University Press. - 1462-0324 .- 1462-0332. ; 50:1, s. 204-213
  • Tidskriftsartikel (refereegranskat)abstract
    • Methods. We identified all adult patients with RA (n = 9612), PsA (n = 1417) and other SpA (n = 1652) initiating a first biologic therapy between 1 January 1999 and 31 December 2008, registered in the Swedish Biologics Register (ARTIS), including information on demographics, disease characteristics and 1-year risk of first-line treatment discontinuation. Results. Over calendar time, measures of disease activity at start declined substantially for all indications, and diminished between first-, second- and third-line therapy starts. One-year risks of first-line therapy discontinuation increased. Switchers to anti-TNF and non-TNF biologics had different comorbidities. Despite < 50% drug retention at 5 years, most patients remained exposed to some biologic. Conclusions. The trends in baseline characteristics and drug retention underscores that any effects of biologics, including comparison between different biologics, must be interpreted in light of the characteristics of the population treated. The observed differences further call for continued vigilance to properly evaluate the safety profiles of biologic treatments as they are currently used. Exposure to multiple biologics presents a challenge for attribution of long-term effects.
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6.
  • Bayat, J. T., et al. (författare)
  • Daily life impact of malocclusion in Swedish adolescents: A grounded theory study
  • 2013
  • Ingår i: Acta Odontologica Scandinavica. - 0001-6357 .- 1502-3850. ; 71:3-4, s. 792-798
  • Tidskriftsartikel (refereegranskat)abstract
    • Objective. To explore how malocclusions affect daily life in adolescents and how adolescents cope with malocclusion-related distress. Materials and methods. Twelve strategically selected teenagers, seven girls and five boys aged 13-14 years, participated in this study. Open, tape-recorded in-depth interviews based on Focus Group Discussions (FGD) were performed using a theme guide and analyzed according to the qualitative method of classic grounded theory (GT). Results. A core category was identified and named 'Repeatedly reminded of the malocclusion'. Associated to the core category, five categories were generated and labeled 'Being directed by the media's ideal image', 'Monitoring others' teeth', 'Struggling with low self-esteem', 'Hiding one's teeth' and 'Striving for cure'. Low self-esteem appeared to be frequently reinforced through the concerns for the malocclusion and handled via different coping strategies, such as hiding the teeth and striving to receive orthodontic treatment. Such processes were further enforced through the influence of media. Low self-esteem could be associated to a visible malposition of teeth, according to the informants. Having to wait for orthodontic treatment was frustrating the adolescents. Conclusions. Adolescents with malocclusion are often reminded of their condition, which can lead to avoiding strategies to minimize the negative feelings associated with the teeth and low self-esteem. Clinicians may therefore need to be aware of potential irrational behaviors when interacting with adolescents with malocclusions. The findings also suggest that there might be a discrepancy of attitudes between professionals focusing on oral health aspects of malocclusions and the adolescents focusing on esthetic aspects.
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7.
  • Ekeus, C., et al. (författare)
  • Preterm birth, social disadvantage, and cognitive competence in Swedish 18- to 19-year-old men
  • 2010
  • Ingår i: Pediatrics. - 0031-4005 .- 1098-4275. ; 125:1, s. e67-73
  • Tidskriftsartikel (refereegranskat)abstract
    • OBJECTIVE: The aim was to study the impact of a range of gestationalages (GAs) on cognitive competence in late adolescence and howthis effect is modified by contextual social adversity in childhood. METHODS: This was a register study based on a national cohortof 119664 men born in Sweden from 1973 to 1976. Data on GA andother perinatal factors were obtained from the Medical BirthRegister, and information on cognitive test scores was extractedfrom military conscription at the ages of 18 to 19 years. Testscores were analyzed as z scores on a 9-point stanine scale,whereby each unit is equivalent to 0.5 SD. Socioeconomic indicatorsof the childhood household were obtained from the Populationand Housing Census of 1990. The data were analyzed by multivariatelinear regression. RESULTS: The mean cognitive test scores decreased in a stepwisemanner with GA. In unadjusted analysis, the test scores were0.63 stanine unit lower in men who were born after 24 to 32gestational weeks than in those who were born at term. The differencein global scores between the lowest and highest category ofsocioeconomic status was 1.57. Adjusting the analysis for thechildhood socioeconomic indicators decreased the effect of GAon cognitive test scores by 26% to 33%. There was also a multiplicativeinteraction effect of social adversity and moderately pretermbirth on cognitive test scores. CONCLUSIONS: This study confirms previous claims of an incrementalassociation of cognitive competence with GA. Socioeconomic indicatorsin childhood modified this effect at all levels of preterm birth.
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8.
  • Eriksson, D, et al. (författare)
  • Extended exome sequencing identifies BACH2 as a novel major risk locus for Addison's disease
  • 2016
  • Ingår i: Journal of Internal Medicine. - : Wiley: 12 months. - 0954-6820 .- 1365-2796. ; 286:6, s. 595-608
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Autoimmune disease is one of the leading causes of morbidity and mortality worldwide. In Addison's disease, the adrenal glands are targeted by destructive autoimmunity. Despite being the most common cause of primary adrenal failure, little is known about its aetiology.METHODS: To understand the genetic background of Addison's disease, we utilized the extensively characterized patients of the Swedish Addison Registry. We developed an extended exome capture array comprising a selected set of 1853 genes and their potential regulatory elements, for the purpose of sequencing 479 patients with Addison's disease and 1394 controls.RESULTS: We identified BACH2 (rs62408233-A, OR = 2.01 (1.71-2.37), P = 1.66 × 10(-15) , MAF 0.46/0.29 in cases/controls) as a novel gene associated with Addison's disease development. We also confirmed the previously known associations with the HLA complex.CONCLUSION: Whilst BACH2 has been previously reported to associate with organ-specific autoimmune diseases co-inherited with Addison's disease, we have identified BACH2 as a major risk locus in Addison's disease, independent of concomitant autoimmune diseases. Our results may enable future research towards preventive disease treatment.
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9.
  • Genereux, Diane P., et al. (författare)
  • A comparative genomics multitool for scientific discovery and conservation
  • 2020
  • Ingår i: Nature. - : NATURE RESEARCH. - 0028-0836 .- 1476-4687. ; 587:7833, s. 240-245
  • Tidskriftsartikel (refereegranskat)abstract
    • A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal-including 131 previously uncharacterized species-from the Zoonomia Project provides data that support biological discovery, medical research and conservation. The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.
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10.
  • Helgadottir, Anna, et al. (författare)
  • Apolipoprotein(a) Genetic Sequence Variants Associated With Systemic Atherosclerosis and Coronary Atherosclerotic Burden But Not With Venous Thromboembolism
  • 2012
  • Ingår i: Journal of the American College of Cardiology. - : Elsevier USA. - 0735-1097 .- 1558-3597. ; 60:8, s. 722-729
  • Tidskriftsartikel (refereegranskat)abstract
    • Objectives The purpose of this study is investigate the effects of variants in the apolipoprotein(a) gene (LPA) on vascular diseases with different atherosclerotic and thrombotic components. Background It is unclear whether the LPA variants rs10455872 and rs3798220, which correlate with lipoprotein(a) levels and coronary artery disease (CAD), confer susceptibility predominantly via atherosclerosis or thrombosis. Methods The 2 LPA variants were combined and examined as LPA scores for the association with ischemic stroke (and TOAST [Trial of Org 10172 in Acute Stroke Treatment] subtypes) (effective sample size [n(e)] = 9,396); peripheral arterial disease (n(e) = 5,215); abdominal aortic aneurysm (ne = 4,572); venous thromboembolism (ne = 4,607); intracranial aneurysm (ne = 1,328); CAD (n(e) = 12,716), carotid intima-media thickness (n = 3,714), and angiographic CAD severity (n = 5,588). Results LPA score was associated with ischemic stroke subtype large artery atherosclerosis (odds ratio [OR]: 1.27; p = 6.7 X 10(-4)), peripheral artery disease (OR: 1.47; p = 2.9 x 10(-14)), and abdominal aortic aneurysm (OR: 1.23; p = 6.0 x 10(-5)), but not with the ischemic stroke subtypes cardioembolism (OR: 1.03; p = 0.69) or small vessel disease (OR: 1.06; p = 0.52). Although the LPA variants were not associated with carotid intima-media thickness, they were associated with the number of obstructed coronary vessels (p = 4.8 x 10(-12)). Furthermore, CAD cases carrying LPA risk variants had increased susceptibility to atherosclerotic manifestations outside of the coronary tree (OR: 1.26; p = 0.0010) and had earlier onset of CAD (-1.58 years/allele; p = 8.2 x 10(-8)) than CAD cases not carrying the risk variants. There was no association of LPA score with venous thromboembolism (OR: 0.97; p = 0.63) or intracranial aneurysm (OR: 0.85; p = 0.15). Conclusions LPA sequence variants were associated with atherosclerotic burden, but not with primarily thrombotic phenotypes. (J Am Coll Cardiol 2012; 60: 722-9) (C) 2012 by the American College of Cardiology Foundation
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