Plasma proteomic associations with genetics and health in the UK Biobank

The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics1.

Genome-wide association study of chronic sputum production implicates loci involved in mucus production and infection

BACKGROUND

Chronic sputum production impacts on quality of life and is a feature of many respiratory diseases. Identification of the genetic variants associated with chronic sputum production in a disease agnostic sample could improve understanding of its causes and identify new molecular targets for treatment.

METHODS

We conducted a genome-wide association study (GWAS) of chronic sputum production in UK Biobank. Signals meeting genome-wide significance (p<5×10-8) were investigated in additional independent studies, were fine-mapped and putative causal genes identified by gene expression analysis. GWASs of respiratory traits were interrogated to identify whether the signals were driven by existing respiratory disease among the cases and variants were further investigated for wider pleiotropic effects using phenome-wide association studies (PheWASs).

RESULTS

From a GWAS of 9714 cases and 48 471 controls, we identified six novel genome-wide significant signals for chronic sputum production including signals in the human leukocyte antigen (HLA) locus, chromosome 11 mucin locus (containing MUC2, MUC5AC and MUC5B) and FUT2 locus. The four common variant associations were supported by independent studies with a combined sample size of up to 2203 cases and 17 627 controls. The mucin locus signal had previously been reported for association with moderate-to-severe asthma. The HLA signal was fine-mapped to an amino acid change of threonine to arginine (frequency 36.8%) in HLA-DRB1 (HLA-DRB1*03:147). The signal near FUT2 was associated with expression of several genes including FUT2, for which the direction of effect was tissue dependent. Our PheWAS identified a wide range of associations including blood cell traits, liver biomarkers, infections, gastrointestinal and thyroid-associated diseases, and respiratory disease.

CONCLUSIONS

Novel signals at the FUT2 and mucin loci suggest that mucin fucosylation may be a driver of chronic sputum production even in the absence of diagnosed respiratory disease and provide genetic support for this pathway as a target for therapeutic intervention.

Asthma control among treated US asthma patients in Practice Fusion's electronic medical record research database

This study investigated burden of 'not well-controlled' asthma, overall and by Global Initiative for Asthma (GINA) Step, among treated asthma patients in Practice Fusion's research database. Asthma control (Asthma Control Test [ACT]) was stratified by GINA Step; prevalence ratios were estimated using Poisson regression with robust variance controlled for confounders. ACT scores ≤19 reflect not well-controlled; >19 reflect 'well-controlled' asthma. Of 15,579 patients, 30% had not well-controlled asthma at index date. The proportion of patients with not well-controlled asthma increased from GINA Step 1 (29%) to Step 5 (45%). Compared with Step 1, the proportion of patients with not well-controlled asthma was 0.87-times lower in Step 2, 1.10-times greater in Step 4, and 1.37-times greater in Step 5. Results suggest that despite available treatments, patients remain symptomatic across GINA Steps in real-world primary care and specialist outpatient practices, with incremental disease burden and unmet medical need in these populations.

Effect of case and control definitions on genome-wide association study (GWAS) findings

Genome-wide association studies (GWAS) have significantly advanced our understanding of the genetic underpinnings of diseases, but case and control cohort definitions for a given disease can vary between different published studies. For example, two GWAS for the same disease using the UK Biobank data set might use different data sources (i.e., self-reported questionnaires, hospital records, etc.) or different levels of granularity (i.e., specificity of inclusion criteria) to define cases and controls. The extent to which this variability in cohort definitions impacts the end-results of a GWAS study is unclear. In this study, we systematically evaluated the effect of the data sources used for case and control definitions on GWAS findings. Using the UK Biobank, we selected three diseases-glaucoma, migraine, and iron-deficiency anemia. For each disease, we designed 13 GWAS, each using different combinations of data sources to define cases and controls, and then calculated the pairwise genetic correlations between all GWAS for each disease. We found that the data sources used to define cases for a given disease can have a significant impact on GWAS end-results, but the extent of this depends heavily on the disease in question. This suggests the need for greater scrutiny on how case cohorts are defined for GWAS.

Dietary Potassium Intake and 20-Year All-Cause Mortality in Older Adults: The Rancho Bernardo Study

We examined the association between dietary potassium intake and all-cause and cause-specific mortality among community-dwelling older adults. Potassium intake was assessed with a food frequency questionnaire administered to 1,363 older adults (mean age 71.0 ± 10.6 years). Cox proportional hazard regressions estimated hazard ratios for sex-specific quintiles of calorie-adjusted potassium in relation to all-cause and cause-specific (cardiovascular disease, CVD, and stroke) mortality, adjusting for numerous covariates. There were 855 deaths (63% mortality) during the 20-year follow-up. Relative to the third quintile, potassium intake in the lowest quintile only was associated with increased risk of all-cause mortality (fully-adjusted hazard ratio 1.33; 95% CI 1.06, 1.67). Potassium intake was not significantly associated with CVD or stroke mortality. These results suggest that low potassium intake is associated with increased risk of mortality independent of overall health status. Ensuring adequate potassium in the diet may be an important strategy for reducing risk of earlier mortality among older adults.

Progress in voluntary medical male circumcision for HIV prevention supported by the US President's Emergency Plan for AIDS Relief through 2017: longitudinal and recent cross-sectional programme data

OBJECTIVE

This article provides an overview and interpretation of the performance of the US President's Emergency Plan for AIDS Relief's (PEPFAR's) male circumcision programme which has supported the majority of voluntary medical male circumcisions (VMMCs) performed for HIV prevention, from its 2007 inception to 2017, and client characteristics in 2017.

DESIGN

Longitudinal collection of routine programme data and disaggregations.

SETTING

14 countries in sub-Saharan Africa with low baseline male circumcision coverage, high HIV prevalence and PEPFAR-supported VMMC programmes.

PARTICIPANTS

Clients of PEPFAR-supported VMMC programmes directed at males aged 10 years and above.

MAIN OUTCOME MEASURES

Numbers of circumcisions performed and disaggregations by age band, result of HIV test offer, procedure technique and follow-up visit attendance.

RESULTS

PEPFAR supported a total of 15 269 720 circumcisions in 14 countries in Southern and Eastern Africa. In 2017, 45% of clients were under 15 years of age, 8% had unknown HIV status, 1% of those tested were HIV+ and 84% returned for a follow-up visit within 14 days of circumcision.

CONCLUSIONS

Over 15 million VMMCs have been supported by PEPFAR since 2007. VMMC continues to attract primarily young clients. The non-trivial proportion of clients not testing for HIV is expected, and may be reassuring that testing is not being presented as mandatory for access to circumcision, or in some cases reflect test kit stockouts or recent testing elsewhere. While VMMC is extremely safe, achieving the highest possible follow-up rates for early diagnosis and intervention on complications is crucial, and programmes continue to work to raise follow-up rates. The VMMC programme has achieved rapid scale-up but continues to face challenges, and new approaches may be needed to achieve the new Joint United Nations Programme on HIV/AIDS goal of 27 million additional circumcisions through 2020.

Knowledge of HIV serodiscordance, transmission, and prevention among couples in Durban, South Africa

Objective

Couples’ voluntary HIV counseling and testing (CVCT) significantly decreases HIV transmission within couples, the largest risk group in sub-Saharan Africa, but it is not currently offered in most HIV testing facilities. To roll out such an intervention, understanding locale-specific knowledge barriers is critical. In this study, we measured knowledge of HIV serodiscordance, transmission, and prevention before and after receipt of CVCT services in Durban.

Design

Pre- and post-CVCT knowledge surveys were administered to a selection of individuals seeking CVCT services.

Methods

Changes in knowledge scores were assessed with McNemar Chi-square tests for balanced data and generalized estimating equation methods for unbalanced data.

Results

The survey included 317 heterosexual black couples (634 individuals) who were primarily Zulu (87%), unemployed (47%), and had at least a secondary level education (78%). 28% of couples proved to be discordant. Only 30% of individuals thought serodiscordance between couples was possible pre‐CVCT compared to 95% post-CVCT. One-third thought there was at least one benefit of CVCT pre‐CVCT, increasing to 96% post‐CVCT. Overall, there were positive changes in knowledge about HIV transmission and prevention. However, many respondents thought all HIV positive mothers give birth to babies with AIDS (64% pre-CVCT, 59% post-CVCT) and that male circumcision does not protect negative men against HIV (70% pre-CVCT, 67% post-CVCT).

Conclusions

CVCT was well received and was followed by improvements in understanding of discordance, the benefits of joint testing, and HIV transmission. Country-level health messaging would benefit from targeting gaps in knowledge about serodiscordance, vertical transmission, and male circumcision.

Predictors of first follow-up HIV testing for couples' voluntary HIV counseling and testing in Ndola, Zambia

INTRODUCTION

We describe predictors of first follow-up testing for concordant negative and discordant couples seeking joint voluntary HIV counseling and testing in Ndola, Zambia, where cohabiting couples account for an estimated two-thirds of incident HIV infections.

METHODS

Demographic and serostatus data were collected from couples' voluntary HIV testing and counseling and follow-up testing services implemented in government clinics. We calculated follow-up testing rates by serostatus and compared rates before and after the introduction of a Good Health Package (GHP).

RESULTS

The follow-up testing rate from May 2011 to December 2012 was 12.2% for concordant negative (M-F-) couples and 24.5% for discordant (M+F- or M-F+) couples. Significant predictors of follow-up testing in multivariate analyses included increasing age of the man [adjusted odds ratio (aOR) = 1.02 per year] and the woman (aOR = 1.02 per year), and either partner being HIV+ (aOR = 2.57 for HIV+ man, aOR = 1.89 for HIV+ woman). The man (aOR = 1.29) and the couple (aOR = 1.22) having been previously tested for HIV were predictive of follow-up testing among concordant negative couples. Introduction of a GHP increased follow-up testing among discordant (aOR = 2.93) and concordant negative (aOR = 2.06) couples.

CONCLUSIONS

A low-cost GHP, including prevention, screening, and treatment for common causes of morbidity and mortality resulted in increased follow-up testing rates among HIV discordant and concordant negative couples. Overall follow-up testing rates remain low, and efforts to increase these rates are necessary to ensure linkage to combination prevention, reduce HIV transmission within couples, and identify seroconversions promptly. Further investigation of low-cost sustainable incentives and other factors influencing follow-up HIV testing for couples is needed.