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Sökning: WFRF:(Duncanson A) > Karolinska Institutet

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1.
  • Romagnoni, A, et al. (författare)
  • Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
  • 2019
  • Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
  • Tidskriftsartikel (refereegranskat)abstract
    • Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.
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  • Sawcer, Stephen, et al. (författare)
  • Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
  • 2011
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 476:7359, s. 214-219
  • Tidskriftsartikel (refereegranskat)abstract
    • Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis.
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  • Su, Zhan, et al. (författare)
  • Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus.
  • 2012
  • Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 44:10
  • Tidskriftsartikel (refereegranskat)abstract
    • Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (Pcombined=4.09×10(-9); odds ratio (OR)=1.21, 95% confidence interval (CI)=1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (Pcombined=2.74×10(-10); OR=1.14, 95% CI=1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus.
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  • Ball, R, et al. (författare)
  • Engaging New Parents in the Development of a Peer Nutrition Education Model Using Participatory Action Research
  • 2022
  • Ingår i: International journal of environmental research and public health. - : MDPI AG. - 1660-4601. ; 19:1
  • Tidskriftsartikel (refereegranskat)abstract
    • This study investigated the implementation model and research methods of a peer education program for new parents focused on infant feeding and nutrition. Two hundred and sixty-nine parents with an infant aged birth to two years old were invited to become co-researchers in a Participatory Action Research (PAR) study over three years. Data included focus group and online participant meeting transcripts, social media data, correspondence between the implementation team and peer educators, and field notes. All data were consolidated regularly and discussed by project participants and the research team. After each PAR cycle, structured content analysis was conducted, informing the next iteration of the implementation model and research methods. Participating parents were highly engaged in child feeding peer-to-peer education, but felt more effective and comfortable being considered as a child-feeding information resource sharer or ‘champion’ rather than a formal peer educator. Similarly, quantitative data collection was only effective when it was integrated seamlessly into the implementation model. PAR methodology suited the diversity and dynamic real-life study setting, facilitating substantial improvements to the peer nutrition intervention model and data collection methods. Our study demonstrated that a genuine collaboration between health professionals and participants to implement research in practice can achieve both intervention outcomes and research aims.
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  • Duncanson, K., et al. (författare)
  • Impact of weight management nutrition interventions on dietary outcomes in children and adolescents with overweight or obesity : a systematic review with meta-analysis
  • 2021
  • Ingår i: Journal of human nutrition and dietetics. - : Wiley. - 0952-3871 .- 1365-277X. ; 34:1, s. 147-177
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: The impact of obesity interventions on dietary intake in children and adolescents with overweight or obesity is unclear. This systematic review aimed to investigate the impact of the dietary component of weight management interventions on the change in diet in children and adolescents with overweight or obesity.METHODS: Eligible randomised controlled trials (RCTs) published between 1975 and 2020 were identified by a systematic search following Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. Meta-analyses of eligible study outcomes were performed using statistical software. A multilevel random effects model was used with three significant random effects fitted using restricted maximum likelihood estimation.RESULTS: This review identified 109 RCTs, including 95 that reported at least one statistically significant dietary outcome change and 14 reporting no significant dietary change. Results from the meta-analyses (n = 29 studies) indicated that, compared to control groups, intervention groups achieved significantly greater reductions in mean total energy intake at ≤6 months (-194 kcal day-1 , 95% confidence interval = -275.80 to -112.90 kcal day-1 , P < 0.001) and up to 12 months (-112 kcal day-1 95% confidence interval = -218.92 to -5.83 kcal day-1 ) P = 0.038), increases in fruit and/or vegetable intakes over 2-12 months (n = 34, range +0.6 to +1.5 servings day-1 ) and reductions in consumption of sugar-sweetened beverages (n = 28, range -0.25 to -1.5 servings day-1 ) at 4-24 months follow-up.CONCLUSIONS: Obesity interventions with a dietary component have a modest but sustained impact on reducing total energy intake and improving intakes of specific food groups in children and adolescents with overweight or obesity. High quality RCTs that are powered to detect change in diet as a primary outcome are warranted.
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  • Shrewsbury, Vanessa A, et al. (författare)
  • Update of the best practice dietetic management of overweight and obese children and adolescents: a systematic review protocol
  • 2018
  • Ingår i: The JBI Database of Systematic Reviews and Implementation Reports. - 2202-4433. ; 16:7, s. 1495-1502
  • Tidskriftsartikel (refereegranskat)abstract
    • REVIEW QUESTION/OBJECTIVE: To update an existing systematic review series of randomized controlled trials (RCT) that include a dietary intervention for the management of overweight or obesity in children or adolescents. Specifically, the review questions are: In randomized controlled trials of interventions which include a dietary intervention for the management of overweight or obesity in children or adolescents.
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