Models and methods: a perspective of the impact of six IMI translational data-centric initiatives for Alzheimer’s disease and other neuropsychiatric disorders

The Innovative Medicines Initiative (IMI), was a European public–private partnership (PPP) undertaking intended to improve the drug development process, facilitate biomarker development, accelerate clinical trial timelines, improve success rates, and generally increase the competitiveness of European pharmaceutical sector research. Through the IMI, pharmaceutical research interests and the research agenda of the EU are supported by academic partnership and financed by both the pharmaceutical companies and public funds. Since its inception, the IMI has funded dozens of research partnerships focused on solving the core problems that have consistently obstructed the translation of research into clinical success. In this post-mortem review paper, we focus on six research initiatives that tackled foundational challenges of this nature: Aetionomy, EMIF, EPAD, EQIPD, eTRIKS, and PRISM. Several of these initiatives focused on neurodegenerative diseases; we therefore discuss the state of neurodegenerative research both at the start of the IMI and now, and the contributions that IMI partnerships made to progress in the field. Many of the initiatives we review had goals including, but not limited to, the establishment of translational, data-centric initiatives and the implementation of trans-diagnostic approaches that move beyond the candidate disease approach to assess symptom etiology without bias, challenging the construct of disease diagnosis. We discuss the successes of these initiatives, the challenges faced, and the merits and shortcomings of the IMI approach with participating senior scientists for each. Here, we distill their perspectives on the lessons learned, with an aim to positively impact funding policy and approaches in the future

Women’s views on partnership working with midwives during pregnancy and childbirth

This is the Accepted Manuscript version of the following article: Sally Boyle, Hilary Thomas, and Fiona Brooks, ‘Women׳s views on partnership working with midwives during pregnancy and childbirth’, Midwifery, Vol. 32: 21-29, January 2016, which has been published in final form at: https://doi.org/10.1016/j.midw.2015.09.001. This manuscript version is made available under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License CC BY NC-ND 4.0 ( http://creativecommons.org/licenses/by-nc-nd/4.0/ ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.Objective: To explore whether the UK Government agenda for partnership working and choice was realised or desired for women during pregnancy and childbirth. Design: A qualitative study was used to explore women’s experience of partnership working with midwives. Data was generated using a diary interview method throughout pregnancy and birth. Setting: 16 women were recruited from two district general hospitals in the South East of England. Findings: Three themes emerged from the data: organisation of care, relationships and choice. Women described their antenatal care as ‘ticking the box’, with midwives focusing on the biomedical aspects of care but not meeting their psycho-social and emotional needs. Time poverty was a significant factor in this finding. Women rarely described developing a partnership relationship with midwives due to a lack of continuity of care and time in which to formulate such relationships. In contrast women attending birth centres for their antenatal care were able to form relationships with a group of midwives who shared a philosophy of care and had sufficient time in which to meet women’s holistic needs. Most of the women in this study did not feel they were offered the choices as outlined in the national choice agenda (DoH, 2007). Implications for Practice: NHS Trusts should review the models of care available to women to ensure that these are not only safe but support women’s psycho-social and emotional needs as well. Partnership case loading models enable midwives and women to form trusting relationships that empowers women to feel involved in decision making and to exercise choice. Group antenatal and postnatal care models also effectively utilise midwifery time whilst increasing maternal satisfaction and social engagement. Technology should also be used more effectively to facilitate inter-professional communication and to provide a more flexible service to women.Peer reviewe

Remaking the world in our own image: vulnerability, resilience and adaptation as historical discourses

A warming climate and less predictable weather patterns, as well as an expanding urban infrastructure susceptible to geophysical hazards, make the world an increasingly dangerous place, even for those living in high‐income countries. It is an opportune moment, therefore, from the vantage point of the second decade of the twenty‐first century, to review the terms and concepts that have been employed regularly over the past 50 years to assess risk and to measure people's exposure to such events in the light of the wider geopolitical context. In particular, it is useful to examine ‘vulnerability’, ‘resilience’, and ‘adaptation’, the principal theoretical concepts that, from an historical perspective, have dominated disaster studies since the end of the Second World War. In addition, it is valuable to enquire as to the extent to which such discourses were ideological products of their time, which sought to explain societies and their environments from the stance of competing conceptual frameworks

An investigation of the effects of lipid-lowering medications: genome-wide linkage analysis of lipids in the HyperGEN study

BACKGROUND: Use of anti-hyperlipidemic medications compromises genetic analysis because of altered lipid profiles. We propose an empirical method to adjust lipid levels for medication effects so that the adjusted lipid values substitute the unmedicated lipid values in the genetic analysis. RESULTS: Published clinical trials were reviewed for HMG-CoA reductase inhibitors and fibric acid derivatives as mono-drug therapy. HMG-CoA reductase inhibitors showed similar effects in African Americans (AA) and non-African Americans (non-AA) for lowering total cholesterol (TC, -50.7 mg/dl), LDL cholesterol (LDL-C, -48.1 mg/dl), and triglycerides (TG, -19.7 mg/dl). Their effect on increasing HDL cholesterol (HDL-C) in AA (+0.4 mg/dl) was lower than in Non-AA (+2.3 mg/dl). The effects of fibric acid derivatives were estimated as -46.1 mg/dl for TC, -40.1 mg/dl for LDL-C, and +5.9 mg/dl for HDL-C in non-AA. The corresponding effects in AA were less extreme (-20.1 mg/dl, -11.4 mg/dl, and +3.1 mg/dl). Similar effect for TG (59.0 mg/dl) was shown in AA and non-AA. The above estimated effects were applied to a multipoint variance components linkage analysis on the lipid levels in 2,403 Whites and 2,214 AA in the HyperGEN study. The familial effects did vary depending on whether the lipids were adjusted for medication use. For example, the heritabilities increased after medication adjustment for TC and LDL-C, but did not change significantly for HDL-C and TG. CONCLUSION: Ethnicity-specific medication adjustments using our empirical method can be employed in epidemiological and genetic analysis of lipids.National Heart, Lung, and Blood Institute (HL554471, HL54472, HL54473, HL54495, HL54496, HL54497, HL54509, HL54515

SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Publisher Copyright: © 2022, The Author(s).Background: Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results: To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions: Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.Peer reviewe

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Funding GMP, PN, and CW are supported by NHLBI R01HL127564. GMP and PN are supported by R01HL142711. AG acknowledge support from the Wellcome Trust (201543/B/16/Z), European Union Seventh Framework Programme FP7/2007–2013 under grant agreement no. HEALTH-F2-2013–601456 (CVGenes@Target) & the TriPartite Immunometabolism Consortium [TrIC]-Novo Nordisk Foundation’s Grant number NNF15CC0018486. JMM is supported by American Diabetes Association Innovative and Clinical Translational Award 1–19-ICTS-068. SR was supported by the Academy of Finland Center of Excellence in Complex Disease Genetics (Grant No 312062), the Finnish Foundation for Cardiovascular Research, the Sigrid Juselius Foundation, and University of Helsinki HiLIFE Fellow and Grand Challenge grants. EW was supported by the Finnish innovation fund Sitra (EW) and Finska Läkaresällskapet. CNS was supported by American Heart Association Postdoctoral Fellowships 15POST24470131 and 17POST33650016. Charles N Rotimi is supported by Z01HG200362. Zhe Wang, Michael H Preuss, and Ruth JF Loos are supported by R01HL142302. NJT is a Wellcome Trust Investigator (202802/Z/16/Z), is the PI of the Avon Longitudinal Study of Parents and Children (MRC & WT 217065/Z/19/Z), is supported by the University of Bristol NIHR Biomedical Research Centre (BRC-1215–2001) and the MRC Integrative Epidemiology Unit (MC_UU_00011), and works within the CRUK Integrative Cancer Epidemiology Programme (C18281/A19169). Ruth E Mitchell is a member of the MRC Integrative Epidemiology Unit at the University of Bristol funded by the MRC (MC_UU_00011/1). Simon Haworth is supported by the UK National Institute for Health Research Academic Clinical Fellowship. Paul S. de Vries was supported by American Heart Association grant number 18CDA34110116. Julia Ramierz acknowledges support by the People Programme of the European Union’s Seventh Framework Programme grant n° 608765 and Marie Sklodowska-Curie grant n° 786833. Maria Sabater-Lleal is supported by a Miguel Servet contract from the ISCIII Spanish Health Institute (CP17/00142) and co-financed by the European Social Fund. Jian Yang is funded by the Westlake Education Foundation. Olga Giannakopoulou has received funding from the British Heart Foundation (BHF) (FS/14/66/3129). CHARGE Consortium cohorts were supported by R01HL105756. Study-specific acknowledgements are available in the Additional file 32: Supplementary Note. The views expressed in this manuscript are those of the authors and do not necessarily represent the views of the National Heart, Lung, and Blood Institute; the National Institutes of Health; or the U.S. Department of Health and Human Services.Peer reviewedPublisher PD

Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

Abstract Background Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery. Results To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N = 1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3–5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism. Conclusions Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk