Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes

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

Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs

Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial (anterior) cruciate ligament (RCCL) are the most common complex orthopedic traits of dogs and all result in debilitating osteoarthritis. Herein we reanalyzed previously reported data: the Norberg angle (a quantitative measure of HD) in 921 dogs, ED in 113 cases and 633 controls, and RCCL in 271 cases and 399 controls and their genotypes at ~185,000 single nucleotide polymorphisms. A novel fixed and random model with a circulating probability unification (FarmCPU) function, with marker-based principal components and a kinship matrix to correct for population stratification, was used. A Bonferroni correction at p<0.01 resulted in a pgenome of 6.96 ×10-8. Six loci were identified; three for HD and three for RCCL. An associated locus at CFA28:34,369,342 for HD was described in the same dogs using a conventional mixed model. No loci were identified for RCCL in the previous report but the two loci for ED in the previous report did not reach genome-wide significance using the FarmCPU model. These results were supported by simulation which demonstrated that the FarmCPU held no power advantage over the linear mixed model for the ED sample but provided additional power for the HD and RCCL samples. Candidate genes for HD and RCCL are discussed. When using FarmCPU software, we recommend a resampling test, that a positive control be used to determine the optimum pseudo quantitative trait nucleotide-based covariate structure of the model, and a negative control be used consisting of permutation testing and the identical resampling test as for the non-permuted phenotypes

A novel iterative mixed model to remap three complex orthopedic traits in dogs

<div><p>Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial (anterior) cruciate ligament (RCCL) are the most common complex orthopedic traits of dogs and all result in debilitating osteoarthritis. We reanalyzed previously reported data: the Norberg angle (a quantitative measure of HD) in 921 dogs, ED in 113 cases and 633 controls, and RCCL in 271 cases and 399 controls and their genotypes at ~185,000 single nucleotide polymorphisms. A novel fixed and random model with a circulating probability unification (FarmCPU) function, with marker-based principal components and a kinship matrix to correct for population stratification, was used. A Bonferroni correction at p<0.01 resulted in a P< 6.96 ×10⁻⁸. Six loci were identified; three for HD and three for RCCL. An associated locus at CFA28:34,369,342 for HD was described previously in the same dogs using a conventional mixed model. No loci were identified for RCCL in the previous report but the two loci for ED in the previous report did not reach genome-wide significance using the FarmCPU model. These results were supported by simulation which demonstrated that the FarmCPU held no power advantage over the linear mixed model for the ED sample but provided additional power for the HD and RCCL samples. Candidate genes for HD and RCCL are discussed. When using FarmCPU software, we recommend a resampling test, that a positive control be used to determine the optimum pseudo quantitative trait nucleotide-based covariate structure of the model, and a negative control be used consisting of permutation testing and the identical resampling test as for the non-permuted phenotypes.</p></div

The summary of genetic relationships among the breeds with the most individuals and the decay of linkage disequilibrium (LD).

<p>Along the top three principal components of variation, the main breeds are genetically distinct (a, b). The extent of LD, measured as average pair-wise r², drops below 0.3 at 11 kb in multiple populations (c). The marker density plot shows the distribution of marker intervals and 80% of marker intervals are less than 30 kb (d). The genotype data used for principal component calculation and genetic relationship building comes from the biggest dataset for HD [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0176932#pone.0176932.ref011" target="_blank">11</a>].</p

SNPs associated with hip dysplasia (HD) and rupture of the cranial cruciate ligament (RCCL) and positional candidate genes based on the FarmCPU method.

<p>SNPs associated with hip dysplasia (HD) and rupture of the cranial cruciate ligament (RCCL) and positional candidate genes based on the FarmCPU method.</p

Warm and wet conditions in the Arctic region during Eocene Thermal Maximum 2

Several episodes of abrupt and transient warming, each lasting between 50,000 and 200,000 years, punctuated the long-term warming during the Late Palaeocene and Early Eocene (58 to 51 Myr ago) epochs1,2. These hyperthermal events, such as the Eocene Thermal Maximum 2 (EMT2) that took place about 53.5 Myr ago2, are associated with rapid increases in atmospheric CO2 content. However, the impacts of most events are documented only locally86. Here we show, on the basis of estimates from the TEX 86 ′ proxy, that sea surface temperatures rose by 3-5 C in the Arctic Ocean during the EMT2. Dinoflagellate fossils demonstrate a concomitant freshening and eutrophication of surface waters, which resulted in euxinia in the photic zone. The presence of palm pollen implies5 that coldest month mean temperatures over the Arctic land masses were no less than 8 C, in contradiction of model simulations that suggest hyperthermal winter temperatures were below freezing6. In light of our reconstructed temperature and hydrologic trends, we conclude that the temperature and hydrographic responses to abruptly increased atmospheric CO2 concentrations were similar for the ETM2 and the better-described Palaeocene-Eocene Thermal Maximum7,8, 55.5 Myr ago. © 2009 Macmillan Publishers Limited. All rights reserved