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- Howe, LJ, et al.
(author)
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Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects
- 2022
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In: Nature genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 54:65, s. 581-
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Journal article (peer-reviewed)abstract
- Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects.
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| 8. |
- Li, Chen, et al.
(author)
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Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length
- 2020
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In: American Journal of Human Genetics. - : CELL PRESS. - 0002-9297 .- 1537-6605. ; 106:3, s. 389-404
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Journal article (peer-reviewed)abstract
- Leukocyte telomere length (LTL) is a heritable biomarker of genomic aging. In this study, we perform a genome-wide meta-analysis of LTL by pooling densely genotyped and imputed association results across large-scale European-descent studies including up to 78,592 individuals. We identify 49 genomic regions at a false dicovery rate (FDR) < 0.05 threshold and prioritize genes at 31, with five highlighting nucleotide metabolism as an important regulator of LTL. We report six genome-wide significant loci in or near SENP7, MOB1B, CARMIL1 , PRRC2A, TERF2, and RFWD3, and our results support recently identified PARP1, POT1, ATM, and MPHOSPH6 loci. Phenome-wide analyses in >350,000 UK Biobank participants suggest that genetically shorter telomere length increases the risk of hypothyroidism and decreases the risk of thyroid cancer, lymphoma, and a range of proliferative conditions. Our results replicate previously reported associations with increased risk of coronary artery disease and lower risk for multiple cancer types. Our findings substantially expand current knowledge on genes that regulate LTL and their impact on human health and disease.
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| 9. |
- Marttila, S, et al.
(author)
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Methylation status of VTRNA2-1/nc886 is stable across populations, monozygotic twin pairs and in majority of tissues
- 2022
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In: Epigenomics. - : Future Medicine Ltd. - 1750-192X .- 1750-1911. ; 14:18, s. 1105-1124
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Journal article (peer-reviewed)abstract
- Aims & methods: The aim of this study was to characterize the methylation level of a polymorphically imprinted gene, VTRNA2-1/ nc886, in human populations and somatic tissues.48 datasets, consisting of more than 30 tissues and >30,000 individuals, were used. Results: nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, whereas ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle. Conclusion: The nc886 imprint may be established in the oocyte, and, after implantation, the methylation status is stable, excluding a few specific tissues.
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| 10. |
- Parai, Catharina, 1977, et al.
(author)
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Characteristics and predicted outcome of patients lost to follow-up after degenerative lumbar spine surgery
- 2020
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In: European Spine Journal. - : Springer Science and Business Media LLC. - 0940-6719 .- 1432-0932. ; 29, s. 3063-3073
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Journal article (peer-reviewed)abstract
- Purpose The relatively large number of participants lost to follow-up (attrition) in spinal registers calls for studies that investigate the features of these individuals and their possible outcome. The aim was to explore the effect of attrition on patient-reported outcome in patients undergoing degenerative lumbar spine surgery. Three groups were studied: spinal stenosis (LSS), disc herniation (LDH) and degenerative disc disorder (DDD). Methods Patients who underwent surgery for degenerative lumbar spine conditions during 2008-2012 according to registration in the Swespine national register were eligible for the study. Non-respondents were registered in Swespine prior to surgery, but not at follow-up. Swespine data were merged with hospital data from seven Swedish regions (65% of the population), Statistics Sweden, the National Patient Register and the Social Insurance Agency. Baseline characteristics of non-respondents were described and compared to those of the respondents. Coefficients from regression analyses on PROM values for respondents were used to estimate the levels of PROM values for non-respondents, assuming the same effects of baseline characteristics for the two subgroups. Regression analyses were then conducted to identify variables associated with non-response. The results from the regression analyses were used to predict outcomes for patients with the characteristics of a non-respondent. Primary outcome variable in LSS and LDH was Global Assessment for leg pain, and in DDD, Global Assessment for back pain. Results Age, sex, educational level, smoking, living alone, being born outside the EU, previous spine surgery and unexpected events before follow-up were factors that were significantly associated with non-response. Being born inside, the EU was important in all of the studied groups (LSS: OR 0.61p = < 0.000; LDH: OR 0.68p = 0.001; DDD: OR 0.58p = 0.04). For spinal stenosis patients, an unexpected event appeared particularly important (OR 3.40,p = 0.000). The predicted outcome of non-respondents was significantly worse than for respondents (LSS: 75.4% successful outcome vs. 78.7%; LDH: 53.9% vs. 58.2%; DDD: 62.7% vs. 67.5%. P-value in all groups = < 0.000). Conclusion Attrition in Swespine cannot be ignored, as non-respondents were predicted to have worse outcome. The effect of attrition bias should always be considered when contemplating outcome recorded in a quality register with patients lost to follow-up.
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| 11. |
- Parai, Catharina, 1977, et al.
(author)
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ISSLS prize in clinical science 2020: the reliability and interpretability of score change in lumbar spine research
- 2020
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In: European Spine Journal. - : Springer Science and Business Media LLC. - 0940-6719 .- 1432-0932. ; 29, s. 663-669
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Journal article (peer-reviewed)abstract
- Purpose A statistically significant score change of a PROM (Patient-Reported Outcome Measure) can be questioned if it does not exceed the clinically Minimal Important Change (MIC) or the SDC (Smallest Detectable Change) of the particular measure. The aim of the study was to define the SDC of three common PROMs in degenerative lumbar spine surgery: Numeric Rating Scale (NRSBACK/LEG), Oswestry Disability Index (ODI) and Euroqol-5-Dimensions (EQ-5D(INDEX)) and to compare them to their MICs. The transition questions Global Assessment (GA(BACK/LEG)) were also explored. Methods Reliability analyses were performed on a test-retest population of 182 symptomatically stable patients, with similar characteristics as the Swespine registry population, who underwent surgery for degenerative lumbar spine conditions 2017-2018. The MIC values were based on the entire registry (n = 98,732) using the ROC curve method. The ICC for absolute agreement was calculated in a two-way random-effects single measures model. For categorical variables, weighted kappa and exact agreement were computed. Results For the NRS, the SDC exceeded the MIC (NRSBACK:3.6 and 2.7; NRSLEG: 3.7 and 3.2, respectively), while they were of an equal size of 18 for the ODI. The gap between the two estimates was remarkable in the EQ-5D(INDEX), where SDC was 0.49 and MIC was 0.10. The GA(BACK/LEG) showed an excellent agreement between the test and the retest occasion. Conclusion For the tested PROM scores, the changes must be considerable in order to distinguish a true change from random error in degenerative lumbar spine surgery research. Graphic abstract These slides can be retrieved under Electronic Supplementary Material. [GRAPHICS] .
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| 12. |
- Reilev, M, et al.
(author)
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Methodology of the brodalumab assessment of hazards: a multicentre observational safety (BRAHMS) study
- 2023
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In: BMJ open. - : BMJ. - 2044-6055. ; 13:2, s. e066057-
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Journal article (peer-reviewed)abstract
- Safe and effective pharmacological treatment is of paramount importance for treating severe psoriasis. Brodalumab, a monoclonal antibody against interleukin (IL) 17 receptor A, was granted marketing authorisation in the EU in 2017. The European Medicines Agency requested a postauthorisation safety study of brodalumab to address potential safety issues raised during drug development regarding major adverse cardiovascular events, suicidal conduct, cancer and serious infections.Methods and analysisBRodalumab Assessment of Hazards: A Multinational Safety is a multicentre observational safety study of brodalumab running from 2017 to 2029 using population-based healthcare databases from Denmark, Sweden, Norway, Netherlands, Germany and three different centres in Italy. A distributed database network approach is used, such that only aggregate data are exchanged between sites.Two types of designs are used: a case-time-control design to study acute effects of transient treatment and a variation of the new user active comparator design to study the effects of transient or chronic treatment. As comparators, inhibitors of TNF-α, inhibitors of IL-12 and IL-23, and other inhibitors of cytokine IL-17A are included.In the self-controlled case-time-control design, the risk of developing the outcome of interest during periods of brodalumab use is compared within individuals to the risk in periods without use.In the active comparator cohort design, new users of brodalumab are identified and matched to new users of active comparators. Potential baseline confounders are adjusted for by using propensity score modelling. For outcomes that potentially require large cumulative exposure, an adapted active comparator design has been developed.Ethics and disseminationThe study is approved by relevant authorities in Denmark, Norway, Sweden, the Netherlands, Germany and Italy in line with the relevant legislation at each site. Data confidentiality is secured by the distributed network approach. Results will be published in peer-reviewed journals.Trial registration numberEUPAS30280.
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| 13. |
- Reilev, M, et al.
(author)
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Methodology of the brodalumab assessment of hazards: a multicentre observational safety (BRAHMS) study
- 2023
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In: BMJ open. - : BMJ. - 2044-6055. ; 13:2, s. e066057-
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Journal article (peer-reviewed)abstract
- Safe and effective pharmacological treatment is of paramount importance for treating severe psoriasis. Brodalumab, a monoclonal antibody against interleukin (IL) 17 receptor A, was granted marketing authorisation in the EU in 2017. The European Medicines Agency requested a postauthorisation safety study of brodalumab to address potential safety issues raised during drug development regarding major adverse cardiovascular events, suicidal conduct, cancer and serious infections.Methods and analysisBRodalumab Assessment of Hazards: A Multinational Safety is a multicentre observational safety study of brodalumab running from 2017 to 2029 using population-based healthcare databases from Denmark, Sweden, Norway, Netherlands, Germany and three different centres in Italy. A distributed database network approach is used, such that only aggregate data are exchanged between sites.Two types of designs are used: a case-time-control design to study acute effects of transient treatment and a variation of the new user active comparator design to study the effects of transient or chronic treatment. As comparators, inhibitors of TNF-α, inhibitors of IL-12 and IL-23, and other inhibitors of cytokine IL-17A are included.In the self-controlled case-time-control design, the risk of developing the outcome of interest during periods of brodalumab use is compared within individuals to the risk in periods without use.In the active comparator cohort design, new users of brodalumab are identified and matched to new users of active comparators. Potential baseline confounders are adjusted for by using propensity score modelling. For outcomes that potentially require large cumulative exposure, an adapted active comparator design has been developed.Ethics and disseminationThe study is approved by relevant authorities in Denmark, Norway, Sweden, the Netherlands, Germany and Italy in line with the relevant legislation at each site. Data confidentiality is secured by the distributed network approach. Results will be published in peer-reviewed journals.Trial registration numberEUPAS30280.
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| 15. |
- van Dongen, J, et al.
(author)
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DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan
- 2021
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In: Molecular psychiatry. - : Springer Science and Business Media LLC. - 1476-5578 .- 1359-4184. ; 26:6, s. 2148-2162
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Journal article (peer-reviewed)abstract
- DNA methylation profiles of aggressive behavior may capture lifetime cumulative effects of genetic, stochastic, and environmental influences associated with aggression. Here, we report the first large meta-analysis of epigenome-wide association studies (EWAS) of aggressive behavior (N = 15,324 participants). In peripheral blood samples of 14,434 participants from 18 cohorts with mean ages ranging from 7 to 68 years, 13 methylation sites were significantly associated with aggression (alpha = 1.2 × 10−7; Bonferroni correction). In cord blood samples of 2425 children from five cohorts with aggression assessed at mean ages ranging from 4 to 7 years, 83% of these sites showed the same direction of association with childhood aggression (r = 0.74, p = 0.006) but no epigenome-wide significant sites were found. Top-sites (48 at a false discovery rate of 5% in the peripheral blood meta-analysis or in a combined meta-analysis of peripheral blood and cord blood) have been associated with chemical exposures, smoking, cognition, metabolic traits, and genetic variation (mQTLs). Three genes whose expression levels were associated with top-sites were previously linked to schizophrenia and general risk tolerance. At six CpGs, DNA methylation variation in blood mirrors variation in the brain. On average 44% (range = 3–82%) of the aggression–methylation association was explained by current and former smoking and BMI. These findings point at loci that are sensitive to chemical exposures with potential implications for neuronal functions. We hope these results to be a starting point for studies leading to applications as peripheral biomarkers and to reveal causal relationships with aggression and related traits.
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