Lessons Learned on Observed-to-Expected Analysis Using Spontaneous Reports During Mass Vaccination.

During the COVID-19 vaccination campaign, observed-to-expected analysis was used by the European Medicines Agency to contextualise data from spontaneous reports to generate real-time evidence on emerging safety concerns that may impact the benefit-risk profile of COVID-19 vaccines. Observed-to-expected analysis compares the number of cases spontaneously reported for an event of interest after vaccination ('observed') to the 'expected' number of cases anticipated to occur in the same number of individuals had they not been vaccinated. Observed-to-expected analysis is a robust methodology that relies on several assumptions that have been described in regulatory guidelines and scientific literature. The use of observed-to-expected analysis to support the safety monitoring of COVID-19 vaccines has provided valuable insights and lessons on its design and interpretability, which could prove to be beneficial in future analyses. When undertaking an observed-to-expected analysis within the context of safety monitoring, several aspects need attention. In particular, we emphasise the importance of stratified and harmonised data collection both for vaccine exposure and spontaneous reporting data, the need for alignment between coding dictionaries and the crucial role of accurate background incidence rates for adverse events of special interest. While these considerations and recommendations were determined in the context of the COVID-19 mass vaccination setting, they are generalisable in principle.

COVID-19 Vaccines and Heavy Menstrual Bleeding: The Impact of Media Attention on Reporting to EudraVigilance.

BACKGROUND AND OBJECTIVE: During the COVID-19 vaccination campaign, over 34,000 reports of heavy menstrual bleeding following the administration of COVID-19 vaccines originating in the Economic European Area were submitted to EudraVigilance, the European Union database of suspected adverse drug reactions. More than 90% of these reports were sent by consumers while the remaining by healthcare professionals. Public concerns regarding menstruation disorders in COVID-19 vaccinees were also covered by the media. We investigated the impact of media attention on the reporting trends of heavy menstrual bleeding to EudraVigilance. METHODS: We used media outlets published in the Economic European Area on menstrual disorders and COVID-19 vaccines from the beginning of the vaccination campaign in the Economic European Area (1 January, 2021) until December 2022 (i.e., after the regulatory request to add the adverse event to the product information) and spontaneous reports from EudraVigilance. RESULTS: We found that the publication of safety updates from regulatory authorities and subsequent coverage in media outlets preceded increased reporting to EudraVigilance. Furthermore, the heavy menstrual bleeding reported in the cases occurred several weeks or months earlier and were not submitted to the respective date. The analysis suggests that the spikes in reporting of heavy menstrual bleeding were to some extent influenced by media coverage in some countries. CONCLUSIONS: Consumer reporting to the European Union spontaneous data collection system, EudraVigilance, was of high value for regulatory safety reviews, albeit the reporting behaviours were not free of the influence of the media. These sources of information can be investigated to understand the context of safety concerns of public health interest.

Predicting the submission frequency of periodic safety update reports: development and application of the EURD tool.

Introduction: Periodic Safety Update Reports (PSURs) are a key pharmacovigilance tool for the continuous evaluation of the benefit-risk balance of a medicinal product in the post-authorisation phase. The PSUR submission frequency for authorised active substances and combinations of active substances across the EU is individually determined. The objective of this research was the development and application of the EURD tool, a statistical method based on readily available safety data to predict PSUR frequencies and to ensure a consistent risk-based approach. Methods: First, variables considered relevant in determining the PSUR frequency were identified from data sources available at the European Medicines Agency. A subsequent first survey with National Competent Authorities in Europe lead to a prioritisation of identified variables, while a second survey was carried out to propose the PSUR frequencies for a set of substances. Finally, a regression model was built on the information collected, applied to a larger list of substances and its results tested via a third survey with the same experts. Results: The developed EURD tool was applied to the 1,032 EURD list entries with a PSUR assessment deferred to 2025 at the time of the creation of the list in 2012. As the number of procedures would have had a significant impact on the workload for the European Medicines Regulatory Network (EMRN), in a second step the workload impact was estimated after allocating the entries according to their proposed frequency. The analysis suggests that all entries could be reviewed by 2038 by increasing the median workload by 15% (from 868 to 1,000 substances/year). Conclusion: The EURD tool is the first data-driven application for supporting decision making of PSUR frequencies based on relevant active substance safety data. While we illustrated its potential for improving the assignment of PSUR submission frequencies for active substances authorised in the EU, other institutions requiring periodic assessment of safety data and balancing of the resulting workload could benefit from it.

Biomedical consequences of elevated cholesterol-containing lipoproteins and apolipoproteins on cardiovascular and non-cardiovascular outcomes.

BACKGROUND: Higher concentrations of cholesterol-containing low-density lipoprotein (LDL-C) increase the risk of cardiovascular disease (CVD). The association of LDL-C with non-CVD traits remains unclear, as are the possible independent contributions of other cholesterol-containing lipoproteins and apolipoproteins. METHODS: Nuclear magnetic resonance spectroscopy was used to measure the cholesterol content of high density (HDL-C), very low-density (VLDL-C), intermediate-density (IDL-C), as well as low-density lipoprotein fractions, the apolipoproteins Apo-A1 and Apo-B, as well as total triglycerides (TG), remnant-cholesterol (Rem-Chol) and total cholesterol (TC). The causal effects of these exposures were assessed against 33 outcomes using univariable and multivariable Mendelian randomization (MR). RESULTS: The majority of cholesterol containing lipoproteins and apolipoproteins affect coronary heart disease (CHD), carotid intima-media thickness, carotid plaque, C-reactive protein (CRP) and blood pressure. Multivariable MR indicated that many of these effects act independently of HDL-C, LDL-C and TG, the most frequently measured lipid fractions. Higher concentrations of TG, VLDL-C, Rem-Chol and Apo-B increased heart failure (HF) risk; often independently of LDL-C, HDL-C or TG. Finally, a subset of these exposures associated with non-CVD traits such as Alzheimer's disease (AD: HDL-C, LDL-C, IDL-C, Apo-B), type 2 diabetes (T2DM: VLDL-C, IDL-C, LDL-C), and inflammatory bowel disease (IBD: LDL-C, IDL-C). CONCLUSIONS: The cholesterol content of a wide range of lipoprotein and apolipoproteins associate with measures of atherosclerosis, blood pressure, CRP, and CHD, with a subset affecting HF, T2DM, AD and IBD risk. Many of the observed effects appear to act independently of LDL-C, HDL-C, and TG, supporting the targeting of lipid fractions beyond LDL-C for disease prevention.

It is known that increases in the amount of certain fats and proteins in the blood can lead to heart attacks. These increases are also found in people with other diseases. Here, we looked at inherited differences in some fats and proteins in blood to explore whether these could be associated with various diseases. We found that some fats and proteins in blood were associated with heart disease (including heart failure), blood pressure, blockages in blood vessels, and to a lesser extent with diabetes, Alzheimer's disease, and inflammatory bowel disease. These findings suggest that changes to lipids and proteins in the blood might lead to various diseases, including some that are not normally associated with changes in the blood. Monitoring these changes could improve diagnosis and treatment of these diseases.

Safety Monitoring of COVID-19 Vaccines: Perspective from the European Medicines Agency.

Prior to deployment of coronavirus disease 2019 (COVID-19) vaccines in the European Union in 2021, a high vaccine uptake leading to an unprecedented volume of safety data from spontaneous reports and real-world evidence, was anticipated. The European Medicines Agency (EMA) implemented specific activities to ensure enhanced monitoring of emerging vaccine safety information, including intensive monitoring of reports of adverse events of special interest and the use of observed-to-expected analyses. The EMA also commissioned several independent observational studies using a large network of electronic healthcare databases and primary data collection via mobile and web-based applications. This preparedness was key for two high-profile safety signals: thrombosis with thrombocytopenia syndrome (TTS), a new clinical entity associated with adenovirus-vectored vaccines, and myocarditis/pericarditis with messenger RNA vaccines. With no existing case definition nor background rates, the signal of TTS posed particular challenges. Nevertheless, it was rapidly identified, evaluated, contextualized and the risk minimized thanks to close surveillance and an efficient use of available evidence, clinical expertise and flexible regulatory tools. The two signals illustrated the complementarity between spontaneous and real-world data, the former enabling rapid risk identification and communication, the latter enabling further characterization. The COVID-19 pandemic has tremendously enhanced the development of tools and methods to harness the unprecedented volume of safety data generated for the vaccines. Areas for further improvement include the need for better and harmonized data collection across Member States (e.g., stratified vaccine exposure) to support signal evaluation in all population groups, risk contextualization, and safety communication.

Genetic risk and incident venous thromboembolism in middle-aged and older adults following COVID-19 vaccination.

BACKGROUND: COVID-19 vaccination has been associated with increased venous thromboembolism (VTE) risk. However, it is unknown whether genetic predisposition to VTE is associated with an increased risk of thrombosis following vaccination. METHODS: Using data from the UK Biobank, which contains in-depth genotyping and linked vaccination and health outcomes information, we generated a polygenic risk score (PRS) using 299 genetic variants. We prospectively assessed associations between PRS and incident VTE immediately after first- and the second-dose vaccination and among historical unvaccinated cohorts during the pre- and early pandemic. We estimated hazard ratios (HR) for PRS-VTE associations using Cox models. RESULTS: Of 359 310 individuals receiving one dose of a COVID-19 vaccine, 160 327 (44.6%) were males, and the mean age at the vaccination date was 69.05 (standard deviation [SD] 8.04) years. After 28- and 90-days' follow-up, 88 and 299 individuals developed VTE, respectively, equivalent to an incidence rate of 0.88 (95% confidence interval [CI] 0.70-1.08) and 0.92 (0.82-1.04) per 100 000 person-days. The PRS was significantly associated with a higher risk of VTE (HR per 1 SD increase in PRS, 1.41 (1.15-1.73) in 28 days and 1.36 (1.22-1.52) in 90 days). Similar associations were found in the historical unvaccinated cohorts. CONCLUSIONS: The strength of genetic susceptibility with post-COVID-19-vaccination VTE is similar to that seen in historical data. Additionally, the observed PRS-VTE associations were equivalent for adenovirus- and mRNA-based vaccines. These findings suggest that, at the population level, the VTE that occurred after the COVID-19 vaccination has a similar genetic etiology to the conventional VTE.

Therapeutic Targets for Heart Failure Identified Using Proteomics and Mendelian Randomization.

BACKGROUND: Heart failure (HF) is a highly prevalent disorder for which disease mechanisms are incompletely understood. The discovery of disease-associated proteins with causal genetic evidence provides an opportunity to identify new therapeutic targets. METHODS: We investigated the observational and causal associations of 90 cardiovascular proteins, which were measured using affinity-based proteomic assays. First, we estimated the associations of 90 cardiovascular proteins with incident heart failure by means of a fixed-effect meta-analysis of 4 population-based studies, composed of a total of 3019 participants with 732 HF events. The causal effects of HF-associated proteins were then investigated by Mendelian randomization, using cis-protein quantitative loci genetic instruments identified from genomewide association studies in more than 30 000 individuals. To improve the precision of causal estimates, we implemented an Mendelian randomization model that accounted for linkage disequilibrium between instruments and tested the robustness of causal estimates through a multiverse sensitivity analysis that included up to 120 combinations of instrument selection parameters and Mendelian randomization models per protein. The druggability of candidate proteins was surveyed, and mechanism of action and potential on-target side effects were explored with cross-trait Mendelian randomization analysis. RESULTS: Forty-four of ninety proteins were positively associated with risk of incident HF (P<6.0×10-4). Among these, 8 proteins had evidence of a causal association with HF that was robust to multiverse sensitivity analysis: higher CSF-1 (macrophage colony-stimulating factor 1), Gal-3 (galectin-3) and KIM-1 (kidney injury molecule 1) were positively associated with risk of HF, whereas higher ADM (adrenomedullin), CHI3L1 (chitinase-3-like protein 1), CTSL1 (cathepsin L1), FGF-23 (fibroblast growth factor 23), and MMP-12 (matrix metalloproteinase-12) were protective. Therapeutics targeting ADM and Gal-3 are currently under evaluation in clinical trials, and all the remaining proteins were considered druggable, except KIM-1. CONCLUSIONS: We identified 44 circulating proteins that were associated with incident HF, of which 8 showed evidence of a causal relationship and 7 were druggable, including adrenomedullin, which represents a particularly promising drug target. Our approach demonstrates a tractable roadmap for the triangulation of population genomic and proteomic data for the prioritization of therapeutic targets for complex human diseases.

Marketing Authorization Applications Made to the European Medicines Agency in 2018-2019: What was the Contribution of Real-World Evidence?

Information derived from routinely collected real-world data has for a long time been used to support regulatory decision making on the safety of drugs and has more recently been used to support marketing authorization submissions to regulators. There is a lack of detailed information on the use and types of this real-world evidence (RWE) as submitted to regulators. We used resources held by the European Medicines Agency (EMA) to describe the characteristics of RWE included in new marketing authorization applications (MAAs) and extensions of indication (EOIs) for already authorized products submitted to the EMA in 2018 and 2019. For MAAs, 63 of 158 products (39.9%) contained RWE with a total of 117 studies. For 31.7% of these products, the RWE submitted was derived from data collected before the planned authorization. The most common data sources were registries (60.3%) followed by hospital data (31.7%). RWE was mainly included to support safety (87.3%) and efficacy (49.2%) with cohort studies being the most frequently used study design (88.9%). For EOIs, 28 of 153 products (18.3%) contained RWE with a total of 36 studies. For 57.1% of these products, studies were conducted prior to the EOIs. RWE sources were mainly registries (35.6%) and hospital data (27.0%). RWE was typically used to support safety (82.1%) and efficacy (53.6%). Cohort studies were the most commonly used study design (87.6%). We conclude that there is widespread use of RWE to support evaluation of MAAs and EOIs submitted to the EMA and identify areas where further research is required.

Validation of lipid-related therapeutic targets for coronary heart disease prevention using human genetics.

Drug target Mendelian randomization (MR) studies use DNA sequence variants in or near a gene encoding a drug target, that alter the target's expression or function, as a tool to anticipate the effect of drug action on the same target. Here we apply MR to prioritize drug targets for their causal relevance for coronary heart disease (CHD). The targets are further prioritized using independent replication, co-localization, protein expression profiles and data from the British National Formulary and clinicaltrials.gov. Out of the 341 drug targets identified through their association with blood lipids (HDL-C, LDL-C and triglycerides), we robustly prioritize 30 targets that might elicit beneficial effects in the prevention or treatment of CHD, including NPC1L1 and PCSK9, the targets of drugs used in CHD prevention. We discuss how this approach can be generalized to other targets, disease biomarkers and endpoints to help prioritize and validate targets during the drug development process.

Cholesteryl ester transfer protein (CETP) as a drug target for cardiovascular disease.

Development of cholesteryl ester transfer protein (CETP) inhibitors for coronary heart disease (CHD) has yet to deliver licensed medicines. To distinguish compound from drug target failure, we compared evidence from clinical trials and drug target Mendelian randomization of CETP protein concentration, comparing this to Mendelian randomization of proprotein convertase subtilisin/kexin type 9 (PCSK9). We show that previous failures of CETP inhibitors are likely compound related, as illustrated by significant degrees of between-compound heterogeneity in effects on lipids, blood pressure, and clinical outcomes observed in trials. On-target CETP inhibition, assessed through Mendelian randomization, is expected to reduce the risk of CHD, heart failure, diabetes, and chronic kidney disease, while increasing the risk of age-related macular degeneration. In contrast, lower PCSK9 concentration is anticipated to decrease the risk of CHD, heart failure, atrial fibrillation, chronic kidney disease, multiple sclerosis, and stroke, while potentially increasing the risk of Alzheimer's disease and asthma. Due to distinct effects on lipoprotein metabolite profiles, joint inhibition of CETP and PCSK9 may provide added benefit. In conclusion, we provide genetic evidence that CETP is an effective target for CHD prevention but with a potential on-target adverse effect on age-related macular degeneration.

Genetic drug target validation using Mendelian randomisation.

Mendelian randomisation (MR) analysis is an important tool to elucidate the causal relevance of environmental and biological risk factors for disease. However, causal inference is undermined if genetic variants used to instrument a risk factor also influence alternative disease-pathways (horizontal pleiotropy). Here we report how the 'no horizontal pleiotropy assumption' is strengthened when proteins are the risk factors of interest. Proteins are typically the proximal effectors of biological processes encoded in the genome. Moreover, proteins are the targets of most medicines, so MR studies of drug targets are becoming a fundamental tool in drug development. To enable such studies, we introduce a mathematical framework that contrasts MR analysis of proteins with that of risk factors located more distally in the causal chain from gene to disease. We illustrate key model decisions and introduce an analytical framework for maximising power and evaluating the robustness of analyses.

Reevaluating the pathogenicity of the mutation c.1194 +5 G>A in GAA gene by functional analysis of RNA in a 61-year-old woman diagnosed with Pompe disease by muscle biopsy.

Glycogen storage disease type II, or Pompe disease, is an autosomal recessive disorder caused by deficiency of lysosomal acid alpha-glucosidase (GAA). We performed genetic analysis to confirm the diagnosis of Pompe disease in a 61-year-old patient with progressive weakness in extremities, severe Sleep Apnea-Hypopnea Syndrome, a significant reduction of alpha-glucosidase in liquid sample of peripheral blood and muscular biopsy diagnosis. GAA gene sequencing showed the patient is homozygous for the splice-site mutation c.1194+5G>A, considered as nonpathogenic in Pompe Center mutation database. Further molecular RNA characterization of GAA transcripts allowed us to identify abnormal processing of pre-mRNA, leading to aberrant transcripts and a significant reduction of GAA mRNA levels. Our results indicate that c.1194+5G>A is a pathogenic splice-site mutation and should be considered as such for diagnostic purposes. This study emphasizes the potential role of functional studies to determine the consequences of mutations with no evident pathogenicity.

ChEMBL: towards direct deposition of bioassay data.

ChEMBL is a large, open-access bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012, 2014 and 2017 Nucleic Acids Research Database Issues. In the last two years, several important improvements have been made to the database and are described here. These include more robust capture and representation of assay details; a new data deposition system, allowing updating of data sets and deposition of supplementary data; and a completely redesigned web interface, with enhanced search and filtering capabilities.