Reaching the End-Game for GWAS: Machine Learning Approaches for the Prioritization of Complex Disease Loci.

Genome-wide association studies (GWAS) have revealed thousands of genetic loci that underpin the complex biology of many human traits. However, the strength of GWAS - the ability to detect genetic association by linkage disequilibrium (LD) - is also its limitation. Whilst the ever-increasing study size and improved design have augmented the power of GWAS to detect effects, differentiation of causal variants or genes from other highly correlated genes associated by LD remains the real challenge. This has severely hindered the biological insights and clinical translation of GWAS findings. Although thousands of disease susceptibility loci have been reported, causal genes at these loci remain elusive. Machine learning (ML) techniques offer an opportunity to dissect the heterogeneity of variant and gene signals in the post-GWAS analysis phase. ML models for GWAS prioritization vary greatly in their complexity, ranging from relatively simple logistic regression approaches to more complex ensemble models such as random forests and gradient boosting, as well as deep learning models, i.e., neural networks. Paired with functional validation, these methods show important promise for clinical translation, providing a strong evidence-based approach to direct post-GWAS research. However, as ML approaches continue to evolve to meet the challenge of causal gene identification, a critical assessment of the underlying methodologies and their applicability to the GWAS prioritization problem is needed. This review investigates the landscape of ML applications in three parts: selected models, input features, and output model performance, with a focus on prioritizations of complex disease associated loci. Overall, we explore the contributions ML has made towards reaching the GWAS end-game with consequent wide-ranging translational impact

Correlation of influenza infection with glycan array

Poster Presentation: SPB1 / SPB2 - Virus Host Interaction/Pathogensis/Transmission: abstract no. B109PINTRODUCTION: The past 6 years has seen the introduction of glycan arrays containing large numbers of sialic acid (Sia) containing compounds and these arrays have been used to demonstrate the relative binding affinity of influenza viruses to different glycans. Though infor...postprin

Metabolic risk factors and the incidence and progression of radiographic hand osteoarthritis: a population-based cohort study.

OBJECTIVE: To determine whether selected metabolic factors are associated with greater amounts of radiographic hand osteoarthritis (OA) incidence and progression. METHODS: The study identified 706 adults, aged 50-69 years, with hand pain and hand radiographs at baseline, from two population-based cohorts. Metabolic factors (body mass index, hypertension, dyslipidaemia, and diabetes) were ascertained at baseline by direct measurement and medical records. Analyses were undertaken following multiple imputation of missing data, and in complete cases (sensitivity analyses). Multivariable regression models estimated associations between metabolic factors and two measures of radiographic change at 7 years for all participants, individuals free of baseline radiographic OA, and in baseline hand OA subsets. Estimates were adjusted for baseline values and other covariates. RESULTS: The most consistent and strong associations observed were between the presence of diabetes and the amount of radiographic progression in individuals with nodal OA [adjusted mean differences in Kellgren-Lawrence summed score of 4.50 (-0.26, 9.25)], generalized OA [3.27 (-2.89, 9.42)], and erosive OA [3.05 (-13.56, 19.67)]. The remaining associations were generally weak or inconsistent, although numbers were limited for analyses of incident radiographic OA and erosive OA in particular. CONCLUSION: Overall metabolic risk factors were not independently or collectively associated with greater amounts of radiographic hand OA incidence or progression over 7 years, but diabetes was associated with radiographic progression in nodal, and possibly generalized and erosive OA. Diabetes has previously been associated with prevalent but not incident hand OA. Further investigation in hand OA subsets using objective measures accounting for disease duration and control is warranted

Over 1000 genetic loci influencing blood pressure with multiple systems and tissues implicated.

High blood pressure (BP) remains the major heritable and modifiable risk factor for cardiovascular disease. Persistent high BP, or hypertension, is a complex trait with both genetic and environmental interactions. Despite swift advances in genomics, translating new discoveries to further our understanding of the underlying molecular mechanisms remains a challenge. More than 500 loci implicated in the regulation of BP have been revealed by genome-wide association studies (GWAS) in 2018 alone, taking the total number of BP genetic loci to over 1000. Even with the large number of loci now associated to BP, the genetic variance explained by all loci together remains low (~5.7%). These genetic associations have elucidated mechanisms and pathways regulating BP, highlighting potential new therapeutic and drug repurposing targets. A large proportion of the BP loci were discovered and reported simultaneously by multiple research groups, creating a knowledge gap, where the reported loci to date have not been investigated in a harmonious way. Here, we review the BP-associated genetic variants reported across GWAS studies and investigate their potential impact on the biological systems using in silico enrichment analyses for pathways, tissues, gene ontology and genetic pleiotropy

Longitudinal validity of using digital hand photographs for assessing hand osteoarthritis progression over 7 years in community-dwelling older adults with hand pain

Abstract Background : To determine the longitudinal construct validity of assessing hand OA progression on digital photographs over 7 years compared with progression determined from radiographs, clinical features and change in symptoms. Methods: Participants were community-dwelling older adults (≥50 years) in North Staffordshire, UK. Standardized digital hand photographs were taken at baseline and 7 years, and hand joints graded for OA severity using an established photographic atlas. Radiographic hand OA was assessed using the Kellgren and Lawrence grading system. Hand examination determined the presence of nodes, bony enlargement and deformity. Symptoms were reported in self-complete questionnaires. Radiographic and clinical progression and change in symptoms were compared to photographic progression. Differences were examined using analysis of covariance and Chi-Square tests. Results: Of 253 individuals (61% women, mean age 63 years) the proportion with photographic progression at the joint and joint group-level was higher in individuals with radiographic or clinical progression compared to those without, although differences were not statistically significant. At the person-level, those with moderate photographic progression over 7 years had significantly higher summed radiographic and clinical scores (adjusted for baseline scores) compared to those with no or mild photographic progression. Similar findings were observed for change in symptoms, although differences were small and not statistically significant. Conclusion: Assessing hand OA on photographs shows modest longitudinal construct validity over 7 years compared with change in radiographic and clinical hand OA at the person-level. Using photographs to assess overall long-term change in a person with hand OA may be a reasonable alternative when hand examinations and radiographs are not feasible.</jats:p

Future response of global coastal wetlands to sea-level rise.

The response of coastal wetlands to sea-level rise during the twenty-first century remains uncertain. Global-scale projections suggest that between 20 and 90 per cent (for low and high sea-level rise scenarios, respectively) of the present-day coastal wetland area will be lost, which will in turn result in the loss of biodiversity and highly valued ecosystem services1-3. These projections do not necessarily take into account all essential geomorphological4-7 and socio-economic system feedbacks8. Here we present an integrated global modelling approach that considers both the ability of coastal wetlands to build up vertically by sediment accretion, and the accommodation space, namely, the vertical and lateral space available for fine sediments to accumulate and be colonized by wetland vegetation. We use this approach to assess global-scale changes in coastal wetland area in response to global sea-level rise and anthropogenic coastal occupation during the twenty-first century. On the basis of our simulations, we find that, globally, rather than losses, wetland gains of up to 60 per cent of the current area are possible, if more than 37 per cent (our upper estimate for current accommodation space) of coastal wetlands have sufficient accommodation space, and sediment supply remains at present levels. In contrast to previous studies1-3, we project that until 2100, the loss of global coastal wetland area will range between 0 and 30 per cent, assuming no further accommodation space in addition to current levels. Our simulations suggest that the resilience of global wetlands is primarily driven by the availability of accommodation space, which is strongly influenced by the building of anthropogenic infrastructure in the coastal zone and such infrastructure is expected to change over the twenty-first century. Rather than being an inevitable consequence of global sea-level rise, our findings indicate that large-scale loss of coastal wetlands might be avoidable, if sufficient additional accommodation space can be created through careful nature-based adaptation solutions to coastal management.Personal research fellowship of Mark Schuerch (Project Number 272052902) and by the Cambridge Coastal Research Unit (Visiting Scholar Programme). Furthermore, this work has partly been supported by the EU research project RISES-AM- (FP7-ENV-693396)

Eurasian Tree Sparrows, Risk for H5N1 Virus Spread and Human Contamination through Buddhist Ritual: An Experimental Approach

Background: The Highly Pathogenic Avian Influenza H5N1 virus has dramatically spread throughout Southeast Asia since its first detection in 1997. Merit Release Birds, such as the Eurasian Tree Sparrow, are believed to increase one's positive karma when kissed and released during Buddhist rituals. Since these birds are often in close contact with both poultry and humans, we investigated their potential role in the spread of H5N1 virus. Methodology/Principal Findings: Seven series of experiments were conducted in order to investigate the possible interactions between inoculated and exposed birds, including sparrow/sparrow, sparrow/chicken, duck/sparrow. Daily and post-mortem samples collected were tested for H5N1 virus by real-time RT-PCR and egg inoculation. When directly inoculated, Eurasian Tree Sparrows were highly susceptible to the H5N1 virus, with a fatality rate approaching 100% within 5 days post-inoculation. Although transmission of fatal infection between sparrows did not occur, seroconversion of the exposed birds was observed. Up to 100% chickens exposed to inoculated sparrows died of H5N1 infection, depending on the caging conditions of the birds, while a fatality rate of 50% was observed on sparrows exposed to infected ducks. Large quantities of H5N1 virus were detected in the sparrows, particularly in their feathers, from which infectious particles were recovered. Conclusions/Significance: Our study indicates that under experimental conditions, Eurasian Tree Sparrows are susceptible to H5N1 infection, either by direct inoculation or by contact with infected poultry. Their ability to transmit H5N1 infection to other birds is also demonstrated, suggesting that the sparrows may play a role in the dissemination of the virus. Finally, the presence of significant quantities of H5N1 virus on sparrows' feathers, including infectious particles, would suggest that Merit Release Birds represent a risk for human contamination in countries where avian influenza virus is circulating and where this religious ritual is practiced. © 2011 Gutiérrez et al.published_or_final_versio

Hemagglutinin-neuraminidase balance confers respiratory-droplet transmissibility of the Pandemic H1N1 Influenza virus in ferrets

Conference Theme: Translating Health Research into Policy and Practice for Health of the PopulationPoster Presentations: Emerging / Infectious Diseases: no. P66-Ab0011published_or_final_versio