1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function

HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10(-8) previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, which were missed by our previous analyses. Among those, the 10 identified novel genes are part of pathways of kidney development, carbohydrate metabolism, cardiac septum development and glucose metabolism. These results highlight the utility of re-imputing from denser reference panels, until whole-genome sequencing becomes feasible in large samples

Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney.

Elevated blood pressure is a major risk factor for cardiovascular disease and has a substantial genetic contribution. Genetic variation influencing blood pressure has the potential to identify new pharmacological targets for the treatment of hypertension. To discover additional novel blood pressure loci, we used 1000 Genomes Project-based imputation in 150 134 European ancestry individuals and sought significant evidence for independent replication in a further 228 245 individuals. We report 6 new signals of association in or near HSPB7, TNXB, LRP12, LOC283335, SEPT9, and AKT2, and provide new replication evidence for a further 2 signals in EBF2 and NFKBIA Combining large whole-blood gene expression resources totaling 12 607 individuals, we investigated all novel and previously reported signals and identified 48 genes with evidence for involvement in blood pressure regulation that are significant in multiple resources. Three novel kidney-specific signals were also detected. These robustly implicated genes may provide new leads for therapeutic innovation

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.

Elevated serum urate levels cause gout and correlate with cardiometabolic diseases via poorly understood mechanisms. We performed a trans-ancestry genome-wide association study of serum urate in 457,690 individuals, identifying 183 loci (147 previously unknown) that improve the prediction of gout in an independent cohort of 334,880 individuals. Serum urate showed significant genetic correlations with many cardiometabolic traits, with genetic causality analyses supporting a substantial role for pleiotropy. Enrichment analysis, fine-mapping of urate-associated loci and colocalization with gene expression in 47 tissues implicated the kidney and liver as the main target organs and prioritized potentially causal genes and variants, including the transcriptional master regulators in the liver and kidney, HNF1A and HNF4A. Experimental validation showed that HNF4A transactivated the promoter of ABCG2, encoding a major urate transporter, in kidney cells, and that HNF4A p.Thr139Ile is a functional variant. Transcriptional coregulation within and across organs may be a general mechanism underlying the observed pleiotropy between urate and cardiometabolic traits.The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Variant annotation was supported by software resources provided via the Caché Campus program of the InterSystems GmbH to Alexander Teumer

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function

HapMap imputed genome-wide association studies (GWAS) have revealed > 50 loci at which common variants with minor allele frequency > 5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 x 10(-8) previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, which were missed by our previous analyses. Among those, the 10 identified novel genes are part of pathways of kidney development, carbohydrate metabolism, cardiac septum development and glucose metabolism. These results highlight the utility of re-imputing from denser reference panels, until wholegenome sequencing becomes feasible in large samples

Evidence of Inbreeding Depression on Human Height

WOS:000306840400001Peer reviewe

1000 Genomes-based metaanalysis identifies 10 novel loci for kidney function

HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-Analysis of kidney function based on the estimated glomerular filtration rate (EGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10-8 previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, wh

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Chimie induite par électrons lents (0-20 eV) au sein de films moléculaires supportés

High-energy irradiation of condensed matter leads to the production of copious amounts of low-energy (0-20 eV) secondary electrons. These electrons are known to trigger various dissociative processes leading to observed damages including erosion and chemical modifications. The resulting reactive species within the condensed media can also lead to the synthesis of new molecules. This has implications in several applications most especially in the design of lithographic methods, focused beam-assisted deposition, as well as in astrochemistry. In all these applications, it is important to identify the processes induced by low-energy electrons, study the reactive fragments and stable molecules produced to determine possibilities of controlling them, and generate quantitative data to gauge the efficiencies of these processes. The approach developed for this PhD work consists of directly irradiating surfaces and interfaces using low-energy electrons and studying the processes that arise. The responses of different model molecular films (of varying thickness) were studied as a function of incident electron energy and dose. In favorable cases, methodologies proposed herein can be used to estimate effective cross sections of observed processes. Three complementary surface-sensitive techniques were utilized for this purpose. To characterize the deposited films and formed residues, the High Resolution Electron-Energy Loss Spectroscopy (HREELS) and Temperature Programmed Desorption (TPD) were used. Neutral fragments (as opposed to their often-detected ionic counterparts) desorbing under electron irradiation were monitored using a mass spectrometer in a technique called Electron Stimulated Desorption (ESD).Within the context of surface functionalization, the grafting of sp2-hybridized carbon centers on a polycrystalline hydrogenated diamond substrate was realized through electron irradiation of a thin layer of benzylamine precursor deposited on its surface. At 11 eV, the dominant mechanism is proposed to be neutral dissociation of the precursor molecules. The effective cross section of the grafting process was estimated in only a single measurement from the HREELS map of the sample surface, taking advantage of the electron beam profile. Within the context of astrochemistry, on the other hand, the responses of crystalline and amorphous NH3 ices were studied under electron impact. The desorption of intact NH3 was observed which resulted in the direct erosion of the film proceeding through a mechanism consistent with desorption induced by electronic transitions (DIET). Different fragmentation and recombination processes were also observed as evidenced by detected neutral species like NHx (x=1,2), N2, and H2. Aside from desorption, a wealth of chemical processes was also observed at 13 eV. Temporal ESD at this energy allowed for the estimation of the effective cross section of NH3 desorption and observing the delayed desorption of N2 and H2. TPD analysis of the residues also provided evidence of N2H2 and N2H4 synthesis in the film. These results can help explain the observed discrepancies in abundances of NH3 and N2 in dense regions in space. Lastly, this PhD work will present prospects for these electron-induced processes to be constrained spatially in microscopic dimensions for lithographic applications. The feasibility of the procedure utilizing Low-Energy Electron Microscope (LEEM) was demonstrated on a terphenylthiol self-assembled monolayer (TPT SAM) specimen. Spots of 5 μm in diameter with different work functions were imprinted on the surface using energies from 10-50 eV. Electron-induced reactions in thin-film resists (PMMA, poly(methyl methacrylate)) were also studied at low-energy identifying opportunities for energy- and spatially-resolved surface modification.Lorsque la matière condensée est soumise à des rayonnements de haute énergie, des électrons secondaires de basse énergie (0-20 eV) sont produits en grande quantité. Ces électrons participent à part entière aux dommages induits dans la matière, incluant les processus d’érosion et de modifications chimiques. Les fragments produits au sein du milieu réagissent et de nouvelles espèces sont formées. Plusieurs domaines d’application sont concernés par ces processus, et plus particulièrement le design de dispositifs par lithographie ou par dépôts assistés par faisceaux focalisés et l’astrochimie. Les enjeux concernent l’identification des mécanismes induits par les électrons lents, le contrôle des fragments réactifs et espèces stables formés, ainsi que la détermination de grandeurs quantitatives permettant d’apprécier l’efficacité des processus impliqués. L’approche développée dans ce travail de thèse consiste à irradier des surfaces et interfaces directement avec des faisceaux d’électrons de basse énergie afin d’étudier les processus induits. Les réponses de films moléculaires supportés modèles (d’épaisseur variable) sont étudiées en fonction de l’énergie incidente des électrons et des doses délivrées. Dans les cas favorables, des méthodologies ont pu être proposées pour accéder à l’estimation de sections efficaces effectives. Pour ce faire, trois techniques expérimentales sont combinées. Les films déposés et les résidus formés sont analysés par spectroscopie de perte d'énergie d’électrons à haute résolution (HREELS) et désorption programmée en température (TPD). Les fragments neutres (et non pas ioniques comme le plus souvent) désorbant sous irradiation sont analysés en masse afin de mener une étude de désorption stimulée par impact d’électrons (ESD).Dans le contexte de la fonctionnalisation de surface, le greffage de centres carbonés hybridés sp2 sur un substrat de diamant poly-cristallin hydrogéné a été réalisé par irradiation électronique d’une couche mince de benzylamine. A 11 eV, le mécanisme dominant implique la dissociation en neutres du précurseur. La section efficace effective de greffage a pu être déterminée par HREELS suite à une unique irradiation, en tirant avantage du profil du faisceau d’irradiation. Dans le contexte de l’astrochimie, la réponse à l’irradiation par électrons lents de glaces d’ammoniac amorphes et cristallisées a été étudiée. La désorption de molécules d’ammoniac a été observée. Elle peut résulter de l’érosion directe du film et de mécanismes de désorption induite par excitation électronique (DIET). Différents processus de fragmentation/recombinaison ont été mis en évidence via la désorption des espèces neutres NHx (x = 1,2), H2 et N2. Une chimie particulièrement riche est induite par irradiation électronique à 13 eV. L’analyse temporelle des rendements ESD a permis la détermination de la section efficace de la désorption de NH3, et l’observation de la formation retardée de N2 et H2. L’analyse TPD des résidus a démontré la synthèse de diazène (N2H2) et d’hydrazine (N2H4) dans le film. Ces résultats peuvent aider à l’élucidation des écarts observés dans les abondances de NH3 et N2 dans les régions denses de l'espace. Enfin, les premiers travaux réalisés pour fonctionnaliser un substrat de façon résolue à l’échelle micrométrique sous irradiation d’électrons lents sont également présentés. La faisabilité de la procédure utilisant un microscope électronique à basse énergie (LEEM) a été démontré sur une monocouche de terphenylthiol (TPT). Des motifs de 5 μm de travaux de sortie différents ont été imprimés en travaillant à des énergies de 10-50 eV. Ensuite la réponse de films modèles de résines lithographiques (PMMA, polyméthacrylate de méthyle) à des irradiations électroniques a été étudiée, afin d’identifier les énergies favorables en vue d’une modification de surface résolue spatialement