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- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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- Colbourne, JK, et al.
(författare)
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The Precision Toxicology initiative
- 2023
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Ingår i: Toxicology letters. - 1879-3169. ; 383, s. 33-42
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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- Niemi, MEK, et al.
(författare)
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- 2021
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- Figlioli, G, et al.
(författare)
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The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer
- 2019
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Ingår i: NPJ breast cancer. - : Springer Science and Business Media LLC. - 2374-4677. ; 5, s. 38-
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Tidskriftsartikel (refereegranskat)abstract
- Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors.
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- Romagnoni, A, et al.
(författare)
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Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
- 2019
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1, s. 10351-
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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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- Sperl, L, et al.
(författare)
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EDUCATIONAL NEEDS AMONG HEALTH PROFESSIONALS IN RHEUMATOLOGY: LOW AWARENESS OF EULAR OFFERINGS AND UNFAMILIARITY WITH COURSE CONTENT AS A MAJOR BARRIER - A EULAR FUNDED EUROPEAN SURVEY
- 2022
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Ingår i: ANNALS OF THE RHEUMATIC DISEASES. - : BMJ. - 0003-4967 .- 1468-2060. ; 81, s. 139-140
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Health professionals in rheumatology (HPRs) should participate in post-graduate or continuous education to update and advance their knowledge and skills. This can improve patient outcomes and increase quality of care.1 EULAR aims to become a leading provider of postgraduate education for HPRs.ObjectivesThe aims of this study were to evaluate the current motivations for participating in postgraduate education of HPRs, identify barriers and facilitators for participation in postgraduate education, and evaluate participation in the current educational offerings of EULAR for HPRs across Europe.MethodsAn online survey was developed and distributed in collaboration with the EULAR Standing Committee of Education and Training (ESCET) and the Paediatric Rheumatology European Society (PReS). The questionnaire was translated by national HPR representatives in 24 languages to cover the 25 national member organisations. Barriers were assessed using 5-point Likert scales, higher scores representing higher barriers. Quantitative data were analysed using descriptive statistics. In addition, we ran the Latent Dirichlet Allocation (LDA) on the answers to the open questions. LDA is an unsupervised probabilistic topic modelling technique that extracts the meanings of a pre-defined number of topics. Design of the survey and reporting of results were done according to the Checklist for Reporting Results of Internet E-Surveys (CHERRIES).ResultsThe online questionnaire was accessed 3,589 times but only 667 complete responses were recorded. HPRs from 34 European countries responded to the survey; 80% of whom were women. The highest-ranked educational need was prevention, including lifestyle interventions and professional development. Although EULAR was well known among HPRs, only 32.1% of HPRs in adult care and 18.6% of HPRs in paediatric care have ever heard of the EULAR School of Rheumatology (Table 1 A).Table 1.A: Feedback on EULAR. Data are presented separately for HPRs in adult and paediatric care; except for the filter questions, no mandatory questions were included in the survey. To clarify the number of responses per question, the number of valid answers for each question was reported.VariablesHPRs in adult careHPRs in paediatric careHave you ever heard of the EULAR School of Rheumatology?61443 I am not sure, n(%)62 (10.1%)7 (16.3%) No, n(%)355 (57.8%)28 (65.1%) Yes, n(%)197 (32.1%)8 (18.6%)Are you aware of courses offered by the EULAR School of Rheumatology? (sub question)1978 I am not sure, n(%)30 (15.2%)2 (25.0%) No, n(%)63 (32.0%)5 (62.5%) Yes, n(%)104 (52.8%)1 (12.5%)Have you ever attended one of the EULAR School of Rheumatology courses? (sub question)1031 I am not sure, n(%)1 (1.0%)0 No, n(%)47 (45.6%)0 Yes, n(%)55 (53.4%)1 (100%)Have you ever participated in a EULAR annual congress meeting?61843 I am not sure, n(%)11 (1.8%)0 No, n(%)457 (73.9%)39 (90.7%) Yes, n(%)150 (24.3%)4 (9.3%)The main barriers to participation in EULAR’s educational offerings were identified by HPRs in adult care and in paediatric care (respectively) as: the unfamiliarity with the course content (3.48 [±1.50]; 3.92 [±1.46]), the associated costs (3.44 [±1.35]; 3.69 [±1.28]) and English language (2.59 [±1.50]; 2.80 [±1.34]).ConclusionEULAR is well-known by HPRs in Europe, however, awareness of educational offerings is low and barriers to participation are numerous. To become the leading provider of postgraduate training by 2023, EULAR could use a “franchise” model that can be tailored to local conditions. This could be achieved by strengthening national organizations by actively involving them in the development of training programs and disseminating these programs and offerings through their networks.References[1]World Health Organization. Health workforce: Education and training: World Health Organization; 2019 [Available from: https://www.who.int/hrh/education/en/ accessed November, 2019 2019.Disclosure of InterestsLisa Sperl: None declared, Tanja Stamm Speakers bureau: AbbVie, Novartis, Roche, Sanofi, and Takeda, Consultant of: AbbVie and Sanofi Genzyme, Grant/research support from: AbbVie and Roche, Margaret Renn Andrews: None declared, Mathilda Bjork: None declared, Carina Boström: None declared, Jeannette Cappon: None declared, Jenny de la Torre-Aboki: None declared, Annette de Thurah: None declared, Andrea Domjan: None declared, Razvan Dragoi Speakers bureau: Received speaker fees last year from: Pfizer, Elly Lilly, Sandoz, Abbvie, Secom, EwoPharma, Fernando Estevez-Lopez: None declared, Ricardo J. O. Ferreira: None declared, George E. Fragoulis: None declared, Jolanta Grygielska: None declared, Katti Korve: None declared, Marja Leena Kukkurainen: None declared, Christel Madelaine-Bonjour: None declared, Andrea Marques: None declared, Jorit Meesters: None declared, Rikke Helene Moe: None declared, Ellen Moholt: None declared, Erika Mosor: None declared, Claudia Naimer-Stach: None declared, Mwidimi Ndosi: None declared, Polina Pchelnikova: None declared, Jette Primdahl: None declared, Polina Putrik: None declared, Anne-Kathrin Rausch Osthoff: None declared, Hana Smucrova: None declared, Sinisa Stefanac: None declared, Marco Testa: None declared, Leti van Bodegom-Vos: None declared, Wilfred Peter: None declared, Heidi A. Zangi: None declared, Olena Zimba: None declared, T.P.M. Vliet Vlieland: None declared, Valentin Ritschl: None declared
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