Εκτίμηση της κατηγορίας μετάδοσης για τους HIV-οροθετικούς με άγνωστη κατηγορία μετάδοσης με μεθόδους μοριακής επιδημιολογίας

Η επιδημία HIV/AIDS παραμένει ακόμα και σήμερα ένα σημαντικό πρόβλημα της δημόσιας υγείας, τόσο σε παγκόσμιο όσο και εθνικό επίπεδο. Ο κίνδυνος μόλυνσης από τον HIV διαφέρει ανάμεσα σε άτομα που ανήκουν σε διαφορετικές κατηγορίες μετάδοσης και επομένως, η γνώση του τρόπου με τον οποίο μεταδόθηκε ο ιός έχει ιδιαίτερη σημασία, καθώς συμβάλει, αφενός, στη βαθύτερη κατανόηση των επιδημιολογικών χαρακτηριστικών της λοίμωξης και αφετέρου, στη λήψη αποτελεσματικότερων μέτρων πρόληψης για τον περιορισμό νέων λοιμώξεων. Παρόλα αυτά, σημαντικό μειονέκτημα στο Εθνικό σύστημα επιδημιολογικής επιτήρησης αποτελεί το μεγάλο ποσοστό των HIV-οροθετικών με ακαθόριστη ομάδα μετάδοσης (18,9%). Σκοπός της παρούσας διπλωματικής εργασίας ήταν η εκτίμηση της κατηγορίας μετάδοσης των HIV-οροθετικών υπότυπου Α1 με ακαθόριστη κατηγορία μετάδοσης. Μελετήθηκαν, συνολικά, 1756 νουκλεοτιδικές αλληλουχίες, που απομονώθηκαν από HIV οροθετικά άτομα υπότυπου Α1, με ημερομηνία διάγνωσης τη χρονική περίοδο 1/2003-6/2015. Από αυτούς, επιλέχθηκαν όλοι οι ασθενείς με ακαθόριστη κατηγορία μετάδοσης (n=196) προκειμένου να διερευνηθεί η πιθανή κατηγορία στην οποία ανήκουν, μέσω μεθόδων φυλογενετικής και φυλογεωγραφικής ανάλυση Η φυλογενετική τοπολογία βασίστηκε σε μεθόδους μέγιστης πιθανοφάνειας με παραμετροποίηση GTR και διακριτή Γ-κατανομή, ενώ η ανάλυση φυλογεωγραφίας στο κριτήριο της μέγιστης φειδωλότητας. Η εκτίμηση της κατηγορίας μετάδοσης βασίστηκε στην εφαρμογή τριών κριτηρίων, Το πρώτο από αυτά πληρούνταν όταν η γενετική απόσταση ανάμεσα στην αλληλουχία ακαθόριστης κατηγορίας μετάδοσης με την πλησιέστερή της αλληλουχία στο φυλογενετικό δέντρο ήταν μικρότερη των 0,015 νουκλεοτιδικών αντικαταστάσεων ανά θέση νουκλεοτιδίου και επομένως, οι ασθενείς που αντιστοιχούσαν στις δύο αυτές αλληλουχίες θεωρούνταν ότι ανήκουν στην ίδια κατηγορία μετάδοσης. Το δεύτερο κριτήριο αφορούσε την εκτίμηση της φυλογεωγραφικής ανάλυσης, θεωρώντας ότι η κατηγορία μετάδοσης του διερευνώμενου ασθενή είναι ίδια με αυτή που προέκυψε από την εκτίμηση της φυλογεωγραφίας για τον πιο πρόσφατο πρόγονο στον πλησιέστερο κόμβο του φυλογενετικού δέντρου. Σε περίπτωση που δεν πληρούνταν τα δύο προηγούμενα κριτήρια, πραγματοποιούνταν αναζήτηση μέσω του HIV-BLAST των 10 και 25 πιο όμοιων γενετικά αλληλουχιών και πραγματοποιούνταν νέα φυλογενετική και φυλογεωγραφική ανάλυση με εφαρμογή των ίδιων κριτηρίων. Η μέθοδος επαναλήφθηκε σε τρία φυλογενετικά δέντρα, διαφορετικά ως προς τις αλληλουχίες αναφοράς, για να περιοριστεί η πιθανότητα εσφαλμένης τοπολογίας. Η αξιοπιστία της μεθόδου, εκτιμήθηκε με τυφλή ανάλυση ευαισθησίας σε 100 τυχαία επιλεγμένους ασθενείς γνωστής ομάδας κινδύνου. Επίσης, ελέγχθηκε, με Χ2 καλής εφαρμογής, αν η μη δήλωση της ομάδας κινδύνου ενός ασθενούς επηρεάζεται από την κατηγορία μετάδοσης στην οποία ανήκει. Τα αποτελέσματα της ανάλυσης ευαισθησίας έδειξαν ότι η ομάδα κινδύνου εκτιμήθηκε στο 86% των περιπτώσεων με ευαισθησία 88,4%. Κατά την κύρια ανάλυση, η κατηγορία μετάδοσης διερευνήθηκε για 196 HIV οροθετικούς και η μέθοδος έδωσε εκτίμηση για το 87,2% των ασθενών, από τους οποίους το 75,44% εκτιμήθηκε ως άντρες με σεξουαλικές επαφές με άνδρες (MSM), το 21,64% ετεροφυλόφιλοι άντρες/γυναίκες και το 2,92% χρήστες ενδοφλέβιων ναρκωτικών. Υπήρχε στατιστικά σημαντική σχέση (p=1,19*10-3) ανάμεσα στην κατηγορία μετάδοσης και τη μη δήλωσή της. Η κατηγορία μετάδοσης των HIV οροθετικούς υπότυπου Α1 με ακαθόριστη κατηγορία μετάδοσης εκτιμήθηκε για ένα αρκετά μεγάλο ποσοστό με ικανοποιητική αξιοπιστία. Η συγκεκριμένη μέθοδος αποτελεί μια πρωτότυπη έρευνα που βασίστηκε σε μεθόδους αιχμής της μοριακής επιδημιολογίας. Τα ευρήματα ενισχύουν τα μέχρι τώρα δεδομένα ότι η επιδημιολογία του HIV στην Ελλάδα αφορά κυρίως MSM και επίσης, βρέθηκε ότι η καταγραφή της ομάδας κινδύνου των χρηστών ενδοφλέβιων ναρκωτικών είναι ικανοποιητική. Τέλος, βρέθηκε ότι η πιθανότητα ένας HIV οροθετικός να δηλωθεί στο εθνικό σύστημα επιδημιολογικής επιτήρησης με ακαθόριστη κατηγορία μετάδοσης φαίνεται πως επηρεάζεται από την κατηγορία μετάδοσης στην οποία ανήκει.HIV/AIDS epidemic still remains a hot issue in the field of both global and local public health. The risk of transmission differs among persons of different transmission groups and thus, the knowledge of transmission route of each patient leads to deeper understanding of viral epidemiology and better preventing measures. Notwithstanding, the percentage of HIV-positive people with undetermined transmission group remains too high (18.9%) in the Hellenic Center for Disease Control and Prevention (HCDCP). The objective of this study was to estimate the transmission group of all HIV-positive patients with undetermined transmission group, who were infected by HIV-1 subsubtype A1. 1756 nucleic acid sequences were analyzed corresponding to HIV-positive persons of sub-subtype A1, who had been diagnosed from January 2003 to June 2015. All patients with undetermined transmission group (n=196) were selected in order to estimate their true transmission group, using phylogenetic and phylogeographic methods. The phylogenetic topology was based on maximum likelihood methods, using GTR evolutionary model and parameters of discrete Gamma-distribution and the phylogeography on maximum parsimony method. Three criteria were used to estimate the transmission group; the first one included the genetic distance between the sequence of undetermined transmission group and its pair on the phylogenetic topology. If the distance was less than 0.015 substitutes per position, then the patients corresponding to these two sequences were considered to be at the same transmission group. According to the second criterion, the transmission group of the investigated patient was given by the estimation of phylogeography at the point of closest node of the sequence. The final criterion included a search of 10 and 25, respectively, genetically closest sequences through HIV-BLAST. Then, a novel phylogenetic and phylogeographic analysis was made implementing the same criteria as before. To reduce the possibility of biased topology, the method was replicated by constructing three phylogenetic trees with different reference sequences. To estimate the reliability of the method, a blinded sensitivity analysis was performed on a sample of 100 patients with known transmission group. A chi-square test was also performed, in order to investigate the association between the transmission group of a patient and its record to the HCDCP. According to the sensitivity analysis results, 88.6% of the transmission group of patients with undetermined transmission group was estimated with 88.4% sensitivity. According to the main analysis results, the transmission group of patients with undetermined transmission group was investigated for 196 HIV-positive individuals and estimated for the 87.2% of them. The 75.44% was estimated as man having sex with men (MSM), the 21.64% as heterosexuals and the 2.92% as injecting drug users (IDU). There was statistically significant association (p=1.19*10-3) between transmission group and its record to HCDCP. A high percent of the transmission group of HIV-positive individuals, infected by sub-subtype A1, with undetermined transmission group was estimated with sufficient reliability. This study forms an innovative researching method based on frontline methods of molecular epidemiology. The study results confirm that the HIV/AIDS epidemic in Greece, mostly, concerns MSM community and that the transmission group recording of IDU is sufficient. Finally, it seems that the probability of an HIV-positive individual to be recorded to HCDCP with undetermined transmission group differs among transmission groups

Genetic analysis of over half a million people characterises C-reactive protein loci

Chronic low-grade inflammation is linked to a multitude of chronic diseases. We report the largest genome-wide association study (GWAS) on C-reactive protein (CRP), a marker of systemic inflammation, in UK Biobank participants (N = 427,367, European descent) and the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium (total N = 575,531 European descent). We identify 266 independent loci, of which 211 are not previously reported. Gene-set analysis highlighted 42 gene sets associated with CRP levels (p ≤ 3.2 ×10−6) and tissue expression analysis indicated a strong association of CRP related genes with liver and whole blood gene expression. Phenome-wide association study identified 27 clinical outcomes associated with genetically determined CRP and subsequent Mendelian randomisation analyses supported a causal association with schizophrenia, chronic airway obstruction and prostate cancer. Our findings identified genetic loci and functional properties of chronic low-grade inflammation and provided evidence for causal associations with a range of diseases

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Blood cells play essential roles in human health, underpinning physiological processes such as immunity, oxygen transport, and clotting, which when perturbed cause a significant global health burden. Here we integrate data from UK Biobank and a large-scale international collaborative effort, including data for 563,085 European ancestry participants, and discover 5,106 new genetic variants independently associated with 29 blood cell phenotypes covering a range of variation impacting hematopoiesis. We holistically characterize the genetic architecture of hematopoiesis, assess the relevance of the omnigenic model to blood cell phenotypes, delineate relevant hematopoietic cell states influenced by regulatory genetic variants and gene networks, identify novel splice-altering variants mediating the associations, and assess the polygenic prediction potential for blood traits and clinical disorders at the interface of complex and Mendelian genetics. These results show the power of large-scale blood cell trait GWAS to interrogate clinically meaningful variants across a wide allelic spectrum of human variation. Analysis of blood cell traits in the UK Biobank and other cohorts illuminates the full genetic architecture of hematopoietic phenotypes, with evidence supporting the omnigenic model for complex traits and linking polygenic burden with monogenic blood diseases

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Blood cells play essential roles in human health, underpinning physiological processes such as immunity, oxygen transport, and clotting, which when perturbed cause a significant global health burden. Here we integrate data from UK Biobank and a large-scale international collaborative effort, including data for 563,085 European ancestry participants, and discover 5,106 new genetic variants independently associated with 29 blood cell phenotypes covering a range of variation impacting hematopoiesis. We holistically characterize the genetic architecture of hematopoiesis, assess the relevance of the omnigenic model to blood cell phenotypes, delineate relevant hematopoietic cell states influenced by regulatory genetic variants and gene networks, identify novel splice-altering variants mediating the associations, and assess the polygenic prediction potential for blood traits and clinical disorders at the interface of complex and Mendelian genetics. These results show the power of large-scale blood cell trait GWAS to interrogate clinically meaningful variants across a wide allelic spectrum of human variation.</p

Online supplementary file 1 - Supplemental material for Treatment With Dupilumab in Patients With Atopic Dermatitis: Systematic Review and Meta-Analysis

Supplemental material, Online supplementary file 1, for Treatment With Dupilumab in Patients With Atopic Dermatitis: Systematic Review and Meta-Analysis by Fotios Koskeridis, Evangelos Evangelou, Evangelia E. Ntzani, Konstantinos Kostikas and Sophia Tsabouri in Journal of Cutaneous Medicine and Surgery</p

Figure S1 - Supplemental material for Treatment With Dupilumab in Patients With Atopic Dermatitis: Systematic Review and Meta-Analysis

Supplemental material, Figure S1, for Treatment With Dupilumab in Patients With Atopic Dermatitis: Systematic Review and Meta-Analysis by Fotios Koskeridis, Evangelos Evangelou, Evangelia E. Ntzani, Konstantinos Kostikas and Sophia Tsabouri in Journal of Cutaneous Medicine and Surgery</p

Associations of genetically predicted fatty acid levels across the phenome: A mendelian randomisation study.

BACKGROUND: Fatty acids are important dietary factors that have been extensively studied for their implication in health and disease. Evidence from epidemiological studies and randomised controlled trials on their role in cardiovascular, inflammatory, and other diseases remains inconsistent. The objective of this study was to assess whether genetically predicted fatty acid concentrations affect the risk of disease across a wide variety of clinical health outcomes. METHODS AND FINDINGS: The UK Biobank (UKB) is a large study involving over 500,000 participants aged 40 to 69 years at recruitment from 2006 to 2010. We used summary-level data for 117,143 UKB samples (base dataset), to extract genetic associations of fatty acids, and individual-level data for 322,232 UKB participants (target dataset) to conduct our discovery analysis. We studied potentially causal relationships of circulating fatty acids with 845 clinical diagnoses, using mendelian randomisation (MR) approach, within a phenome-wide association study (PheWAS) framework. Regression models in PheWAS were adjusted for sex, age, and the first 10 genetic principal components. External summary statistics were used for replication. When several fatty acids were associated with a health outcome, multivariable MR and MR-Bayesian method averaging (MR-BMA) was applied to disentangle their causal role. Genetic predisposition to higher docosahexaenoic acid (DHA) was associated with cholelithiasis and cholecystitis (odds ratio per mmol/L: 0.76, 95% confidence interval: 0.66 to 0.87). This was supported in replication analysis (FinnGen study) and by the genetically predicted omega-3 fatty acids analyses. Genetically predicted linoleic acid (LA), omega-6, polyunsaturated fatty acids (PUFAs), and total fatty acids (total FAs) showed positive associations with cardiovascular outcomes with support from replication analysis. Finally, higher genetically predicted levels of DHA (0.83, 0.73 to 0.95) and omega-3 (0.83, 0.75 to 0.92) were found to have a protective effect on obesity, which was supported using body mass index (BMI) in the GIANT consortium as replication analysis. Multivariable MR analysis suggested a direct detrimental effect of LA (1.64, 1.07 to 2.50) and omega-6 fatty acids (1.81, 1.06 to 3.09) on coronary heart disease (CHD). MR-BMA prioritised LA and omega-6 fatty acids as the top risk factors for CHD. Although we present a range of sensitivity analyses to the address MR assumptions, horizontal pleiotropy may still bias the reported associations and further evaluation in clinical trials is needed. CONCLUSIONS: Our study suggests potentially protective effects of circulating DHA and omega-3 concentrations on cholelithiasis and cholecystitis and on obesity, highlighting the need to further assess them as prevention treatments in clinical trials. Moreover, our findings do not support the supplementation of unsaturated fatty acids for cardiovascular disease prevention

Associations of genetically predicted fatty acid levels across the phenome: A mendelian randomisation study

Background Fatty acids are important dietary factors that have been extensively studied for their implication in health and disease. Evidence from epidemiological studies and randomised controlled trials on their role in cardiovascular, inflammatory, and other diseases remains inconsistent. The objective of this study was to assess whether genetically predicted fatty acid concentrations affect the risk of disease across a wide variety of clinical health outcomes. Methods and findings The UK Biobank (UKB) is a large study involving over 500,000 participants aged 40 to 69 years at recruitment from 2006 to 2010. We used summary-level data for 117,143 UKB samples (base dataset), to extract genetic associations of fatty acids, and individual-level data for 322,232 UKB participants (target dataset) to conduct our discovery analysis. We studied potentially causal relationships of circulating fatty acids with 845 clinical diagnoses, using mendelian randomisation (MR) approach, within a phenome-wide association study (PheWAS) framework. Regression models in PheWAS were adjusted for sex, age, and the first 10 genetic principal components. External summary statistics were used for replication. When several fatty acids were associated with a health outcome, multivariable MR and MR-Bayesian method averaging (MR-BMA) was applied to disentangle their causal role. Genetic predisposition to higher docosahexaenoic acid (DHA) was associated with cholelithiasis and cholecystitis (odds ratio per mmol/L: 0.76, 95% confidence interval: 0.66 to 0.87). This was supported in replication analysis (FinnGen study) and by the genetically predicted omega-3 fatty acids analyses. Genetically predicted linoleic acid (LA), omega-6, polyunsaturated fatty acids (PUFAs), and total fatty acids (total FAs) showed positive associations with cardiovascular outcomes with support from replication analysis. Finally, higher genetically predicted levels of DHA (0.83, 0.73 to 0.95) and omega-3 (0.83, 0.75 to 0.92) were found to have a protective effect on obesity, which was supported using body mass index (BMI) in the GIANT consortium as replication analysis. Multivariable MR analysis suggested a direct detrimental effect of LA (1.64, 1.07 to 2.50) and omega-6 fatty acids (1.81, 1.06 to 3.09) on coronary heart disease (CHD). MR-BMA prioritised LA and omega-6 fatty acids as the top risk factors for CHD. Although we present a range of sensitivity analyses to the address MR assumptions, horizontal pleiotropy may still bias the reported associations and further evaluation in clinical trials is needed. Conclusions Our study suggests potentially protective effects of circulating DHA and omega-3 concentrations on cholelithiasis and cholecystitis and on obesity, highlighting the need to further assess them as prevention treatments in clinical trials. Moreover, our findings do not support the supplementation of unsaturated fatty acids for cardiovascular disease prevention. Loukas Zagkos and colleagues conduct Mendelian randomisation analysis to investigate potential causal associations of circulating fatty acids and 845 disease outcomes in the UK Biobank. Author summary Why was this study done? Epidemiological studies have investigated the influence of dietary fatty acids on several chronic diseases including cardiovascular disease (CVD), inflammatory diseases, cancers, and neurodegenerative conditions. The evidence is conflicting and inconclusive and is not supported by randomised controlled trials (RCTs) on fatty acids supplementation. The fact that the human fatty acid metabolome partly reflects the fatty acid intake was leveraged in this work. What did the researchers do and find? Mendelian randomisation analysis was conducted to investigate potential causal associations of circulating fatty acids and 845 disease outcomes in UK Biobank. We found that 1 mmol/L increase in genetically predicted docosahexaenoic acid (DHA) was associated with 24% reduced odds of cholelithiasis and cholecystitis, as well as 17% reduced odds of obesity. One mmol/L higher genetically predicted linoleic acid (LA) was associated with 27% increased odds of ischemic heart disease. When assessed with other fatty acid classes simultaneously, 1 mmol/L higher genetically predicted LA and omega-6 fatty acids were associated with higher odds of coronary heart disease (64% and 81% increase, respectively). What do these findings mean? Our results support the prioritisation of RCTs examining the role of primary and secondary prevention of cholelithiasis via dietary modification or supplementation of DHA and other omega-3 fatty acids. Our principal findings also provide evidence against the supplemental use of fatty acids for CVD prevention. Triangulation of evidence for causal inference of fatty acid levels through experimental studies susceptible to different assumptions is needed to strengthen the evidence