Dataset Information

Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank.

ABSTRACT: Genome-wide association studies (GWASs) have established the contribution of common and low-frequency variants to metabolic blood measurements in the UK Biobank (UKB). To complement existing GWAS findings, we assessed the contribution of rare protein-coding variants in relation to 355 metabolic blood measurements-including 325 predominantly lipid-related nuclear magnetic resonance (NMR)-derived blood metabolite measurements (Nightingale Health Plc) and 30 clinical blood biomarkers-using 412,393 exome sequences from four genetically diverse ancestries in the UKB. Gene-level collapsing analyses were conducted to evaluate a diverse range of rare-variant architectures for the metabolic blood measurements. Altogether, we identified significant associations (p < 1 × 10^-8) for 205 distinct genes that involved 1,968 significant relationships for the Nightingale blood metabolite measurements and 331 for the clinical blood biomarkers. These include associations for rare non-synonymous variants in PLIN1 and CREB3L3 with lipid metabolite measurements and SYT7 with creatinine, among others, which may not only provide insights into novel biology but also deepen our understanding of established disease mechanisms. Of the study-wide significant clinical biomarker associations, 40% were not previously detected on analyzing coding variants in a GWAS in the same cohort, reinforcing the importance of studying rare variation to fully understand the genetic architecture of metabolic blood measurements.

SUBMITTER: Nag A

PROVIDER: S-EPMC10027475 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank.

Nag Abhishek A Dhindsa Ryan S RS Middleton Lawrence L Jiang Xiao X Vitsios Dimitrios D Wigmore Eleanor E Allman Erik L EL Reznichenko Anna A Carss Keren K Smith Katherine R KR Wang Quanli Q Challis Benjamin B Paul Dirk S DS Harper Andrew R AR Petrovski Slavé S

American journal of human genetics 20230220 3

Genome-wide association studies (GWASs) have established the contribution of common and low-frequency variants to metabolic blood measurements in the UK Biobank (UKB). To complement existing GWAS findings, we assessed the contribution of rare protein-coding variants in relation to 355 metabolic blood measurements-including 325 predominantly lipid-related nuclear magnetic resonance (NMR)-derived blood metabolite measurements (Nightingale Health Plc) and 30 clinical blood biomarkers-using 412,393 ...[more]

PMID: 36809768

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Project description:PurposeThis study aimed to investigate the association between quantitative retinal vascular measurements and the risk of all-cause and premature mortality.MethodsIn this population-based cohort study using the UK Biobank data, we employed the Retina-based Microvascular Health Assessment System to assess fundus images for image quality and extracted 392 retinal vascular measurements per fundus image. These measurements encompass six categories of vascular features: caliber, density, length, tortuosity, branching angle, and complexity. Univariate Cox regression models were used to identify potential indicators of mortality risk using data on all-cause and premature mortality from death registries. Multivariate Cox regression models were then used to test these associations while controlling for confounding factors.ResultsThe final analysis included 66,415 participants. After adjusting for demographic, health, and lifestyle factors and genetic risk score, 18 and 10 retinal vascular measurements were significantly associated with all-cause mortality and premature mortality, respectively. In the fully adjusted model, the following measurements of different vascular features were significantly associated with all-cause mortality and premature mortality: arterial bifurcation density (branching angle), number of arterial segments (complexity), interquartile range and median absolute deviation of arterial curve angle (tortuosity), mean and median values of mean pixel widths of all arterial segments in each image (caliber), skeleton density of arteries in macular area (density), and minimum venular arc length (length).ConclusionsThe study revealed 18 retinal vascular measurements significantly associated with all-cause mortality and 10 associated with premature mortality. Those identified parameters should be further studied for biological mechanisms connecting them to increased mortality risk.Translational relevanceThis study identifies retinal biomarkers for increased mortality risk and provides novel targets for investigating the underlying biological mechanisms.

Project description:BackgroundThe direct effects of general adiposity (body mass index (BMI)) and central adiposity (waist-to-hip-ratio (WHR)) on circulating lipoproteins, lipids, and metabolites are unknown.MethodsWe used new metabolic data from UK Biobank (N=109,532, a five-fold higher N over previous studies). EDTA-plasma was used to quantify 249 traits with nuclear-magnetic-resonance spectroscopy including subclass-specific lipoprotein concentrations and lipid content, plus pre-glycemic and inflammatory metabolites. We used univariable and multivariable two-stage least-squares regression models with genetic risk scores for BMI and WHR as instruments to estimate total (unadjusted) and direct (mutually-adjusted) effects of BMI and WHR on metabolic traits; plus effects on statin use and interaction by sex, statin use, and age (proxy for medication use).FindingsHigher BMI decreased apolipoprotein B and low-density lipoprotein cholesterol (LDL-C) before and after WHR-adjustment, whilst BMI increased triglycerides only before WHR-adjustment. These effects of WHR were larger and BMI-independent. Direct effects differed markedly by sex, e.g., triglycerides increased only with BMI among men, and only with WHR among women. Adiposity measures increased statin use and showed metabolic effects which differed by statin use and age. Among the youngest (38-53y, statins-5%), BMI and WHR (per-SD) increased LDL-C (total effects: 0.04-SD, 95%CI=-0.01,0.08 and 0.10-SD, 95%CI=0.02,0.17 respectively), but only WHR directly. Among the oldest (63-73y, statins-29%), BMI and WHR directly lowered LDL-C (-0.19-SD, 95%CI=-0.27,-0.11 and -0.05-SD, 95%CI=-0.16,0.06 respectively).InterpretationExcess adiposity likely raises atherogenic lipid and metabolite levels exclusively via adiposity stored centrally, particularly among women. Apparent effects of adiposity on lowering LDL-C are likely explained by an effect of adiposity on statin use.FundingUK Medical Research Council; British Heart Foundation; Novo Nordisk; National Institute for Health Research; Wellcome Trust; Cancer Research UK.

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Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank.

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Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank.

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