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Article ; Online: ukbpheno v1.0: An R package for phenotyping health-related outcomes in the UK Biobank.

Yeung, Ming Wai / van der Harst, Pim / Verweij, Niek

STAR protocols

2022 Volume 3, Issue 3, Page(s) 101471

Abstract: The complexity and volume of data associated with population-based cohorts means that generating health-related outcomes can be challenging. Using one such cohort, the UK Biobank-a major open access resource-we present a protocol to efficiently integrate ...

Abstract	The complexity and volume of data associated with population-based cohorts means that generating health-related outcomes can be challenging. Using one such cohort, the UK Biobank-a major open access resource-we present a protocol to efficiently integrate the main dataset and record-level data files, to harmonize and process the data using an R package named "ukbpheno". We describe how to use the package to generate binary phenotypes in a standardized and machine-actionable manner. For complete details on the use and execution of this protocol, please refer to Yeung et al. (2022).
MeSH term(s)	Biological Specimen Banks ; Humans ; Information Storage and Retrieval ; Phenotype ; United Kingdom
Language	English
Publishing date	2022-06-17
Publishing country	United States
Document type	Journal Article
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2022.101471
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Article ; Online: Associations of Observational and Genetically Determined Caffeine Intake With Coronary Artery Disease and Diabetes Mellitus.

Said, M Abdullah / van de Vegte, Yordi J / Verweij, Niek / van der Harst, Pim

Journal of the American Heart Association

2020 Volume 9, Issue 24, Page(s) e016808

Abstract: Background Caffeine is the most widely consumed psychostimulant and is associated with lower risk of coronary artery disease (CAD) and type 2 diabetes mellitus (T2DM). However, whether these associations are causal remains unknown. This study aimed to ... ...

Abstract	Background Caffeine is the most widely consumed psychostimulant and is associated with lower risk of coronary artery disease (CAD) and type 2 diabetes mellitus (T2DM). However, whether these associations are causal remains unknown. This study aimed to identify genetic variants associated with caffeine intake, and to investigate evidence for causal links with CAD or T2DM. In addition, we aimed to replicate previous observational findings. Methods and Results Observational associations were tested within UK Biobank using Cox regression analyses. Moderate observational caffeine intakes from coffee or tea were associated with lower risks of CAD or T2DM, with the lowest risks at intakes of 121 to 180 mg/day from coffee for CAD (hazard ratio [HR], 0.77 [95% CI, 0.73-0.82;
MeSH term(s)	Aged ; Caffeine/administration & dosage ; Caffeine/adverse effects ; Causality ; Coffee/adverse effects ; Coronary Artery Disease/etiology ; Coronary Artery Disease/genetics ; Diabetes Mellitus, Type 2/etiology ; Diabetes Mellitus, Type 2/genetics ; Female ; Genetic Variation ; Genome-Wide Association Study/methods ; Humans ; Male ; Mendelian Randomization Analysis/methods ; Middle Aged ; Proportional Hazards Models ; Risk Factors ; Risk Reduction Behavior ; Tea/adverse effects
Chemical Substances	Coffee ; Tea ; Caffeine (3G6A5W338E)
Language	English
Publishing date	2020-12-08
Publishing country	England
Document type	Journal Article ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2653953-6
ISSN	2047-9980 ; 2047-9980
ISSN (online)	2047-9980
ISSN	2047-9980
DOI	10.1161/JAHA.120.016808
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Article ; Online: Identification of 64 Novel Genetic Loci Provides an Expanded View on the Genetic Architecture of Coronary Artery Disease.

van der Harst, Pim / Verweij, Niek

Circulation research

2017 Volume 122, Issue 3, Page(s) 433–443

Abstract: Rationale: Coronary artery disease (CAD) is a complex phenotype driven by genetic and environmental factors. Ninety-seven genetic risk loci have been identified to date, but the identification of additional susceptibility loci might be important to ... ...

Abstract	Rationale: Coronary artery disease (CAD) is a complex phenotype driven by genetic and environmental factors. Ninety-seven genetic risk loci have been identified to date, but the identification of additional susceptibility loci might be important to enhance our understanding of the genetic architecture of CAD. Objective: To expand the number of genome-wide significant loci, catalog functional insights, and enhance our understanding of the genetic architecture of CAD. Methods and results: We performed a genome-wide association study in 34 541 CAD cases and 261 984 controls of UK Biobank resource followed by replication in 88 192 cases and 162 544 controls from CARDIoGRAMplusC4D. We identified 75 loci that replicated and were genome-wide significant ( Conclusions: We identified 64 novel genetic risk loci for CAD and performed fine mapping of all 161 risk loci to obtain a credible set of causal variants. The large expansion of reconstituted gene sets argues in favor of an expanded omnigenic model view on the genetic architecture of CAD.
MeSH term(s)	3' Untranslated Regions ; Atrial Fibrillation/genetics ; Case-Control Studies ; Causality ; Chromatin/genetics ; Coronary Artery Disease/genetics ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Genome-Wide Association Study ; Heart Failure/genetics ; Humans ; Mutation, Missense ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci
Chemical Substances	3' Untranslated Regions ; Chromatin
Language	English
Publishing date	2017-12-06
Publishing country	United States
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't
ZDB-ID	80100-8
ISSN	1524-4571 ; 0009-7330 ; 0931-6876
ISSN (online)	1524-4571
ISSN	0009-7330 ; 0931-6876
DOI	10.1161/CIRCRESAHA.117.312086
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Article ; Online: Associations of Combined Genetic and Lifestyle Risks With Incident Cardiovascular Disease and Diabetes in the UK Biobank Study.

Said, M Abdullah / Verweij, Niek / van der Harst, Pim

JAMA cardiology

2018 Volume 3, Issue 8, Page(s) 693–702

Abstract: Importance: Genetic and lifestyle factors both contribute to the risk of developing cardiovascular disease, but whether poor health behaviors are associated with similar increases in risk among individuals with low, intermediate, or high genetic risk is ...

Abstract	Importance: Genetic and lifestyle factors both contribute to the risk of developing cardiovascular disease, but whether poor health behaviors are associated with similar increases in risk among individuals with low, intermediate, or high genetic risk is unknown. Objective: To investigate the association of combined health behaviors and factors within genetic risk groups with coronary artery disease, atrial fibrillation, stroke, hypertension, and type 2 diabetes as well as to investigate the interactions between genetic risk and lifestyle. Design, setting, and participants: The UK Biobank cohort study includes more than 500 000 participants aged 40 to 70 years who were recruited from 22 assessment centers across the United Kingdom from 2006 to 2010. A total of 339 003 unrelated individuals of white British descent with available genotype and matching genetic data and reported sex were included in this study from the UK Biobank population-based sample. Individuals were included in the analyses of 1 or more new-onset diseases. Data were analyzed from April 2006 to March 2015. Main outcomes and measures: Risks of new-onset cardiovascular disease and diabetes associated with genetic risk and combined health behaviors and factors. Genetic risk was categorized as low (quintile 1), intermediate (quintiles 2-4), or high (quintile 5). Within each genetic risk group, the risks of incident events associated with ideal, intermediate, or poor combined health behaviors and factors were investigated and compared with low genetic risk and ideal lifestyle. Results: Of 339 003 individuals, 181 702 (53.6%) were female, and the mean (SD) age was 56.86 (7.99) years. During follow-up, 9771 of 325 133 participants (3.0%) developed coronary artery disease, 7095 of 333 637 (2.1%) developed atrial fibrillation, 3145 of 332 971 (0.9%) developed stroke, 11 358 of 234 651 (4.8%) developed hypertension, and 4379 of 322 014 (1.4%) developed diabetes. Genetic risk and lifestyle were independent predictors of incident events, and there were no interactions for any outcome. Compared with ideal lifestyle in the low genetic risk group, poor lifestyle was associated with a hazard ratio of up to 4.54 (95% CI, 3.72-5.54) for coronary artery disease, 5.41 (95% CI, 4.29-6.81) for atrial fibrillation, 4.68 (95% CI, 3.85-5.69) for hypertension, 2.26 (95% CI, 1.63-3.14) for stroke, and 15.46 (95% CI, 10.82-22.08) for diabetes in the high genetic risk group. Conclusions and relevance: In this large contemporary population, genetic composition and combined health behaviors and factors had a log-additive effect on the risk of developing cardiovascular disease. The relative effects of poor lifestyle were comparable between genetic risk groups. Behavioral lifestyle changes should be encouraged for all through comprehensive, multifactorial approaches, although high-risk individuals may be selected based on the genetic risk.
MeSH term(s)	Adult ; Aged ; Atrial Fibrillation/epidemiology ; Atrial Fibrillation/genetics ; Biological Specimen Banks ; Cardiovascular Diseases/epidemiology ; Cardiovascular Diseases/genetics ; Coronary Artery Disease/epidemiology ; Coronary Artery Disease/genetics ; Diabetes Mellitus, Type 2/epidemiology ; Diabetes Mellitus, Type 2/genetics ; Diet ; Exercise ; Female ; Gene-Environment Interaction ; Genetic Predisposition to Disease ; Health Behavior ; Humans ; Hypertension/epidemiology ; Hypertension/genetics ; Incidence ; Life Style ; Male ; Middle Aged ; Proportional Hazards Models ; Risk Factors ; Smoking/epidemiology ; Stroke/epidemiology ; Stroke/genetics ; United Kingdom/epidemiology
Language	English
Publishing date	2018-06-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2380-6591
ISSN (online)	2380-6591
DOI	10.1001/jamacardio.2018.1717
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Article ; Online: Divergent role of Mitochondrial Amidoxime Reducing Component 1 (MARC1) in human and mouse.

Smagris, Eriks / Shihanian, Lisa M / Mintah, Ivory J / Bigdelou, Parnian / Livson, Yuliya / Brown, Heather / Verweij, Niek / Hunt, Charleen / Johnson, Reid O'Brien / Greer, Tyler J / Hartford, Suzanne A / Hindy, George / Sun, Luanluan / Nielsen, Jonas B / Halasz, Gabor / Lotta, Luca A / Murphy, Andrew J / Sleeman, Mark W / Gusarova, Viktoria

PLoS genetics

2024 Volume 20, Issue 3, Page(s) e1011179

Abstract: Recent human genome-wide association studies have identified common missense variants in MARC1, p.Ala165Thr and p.Met187Lys, associated with lower hepatic fat, reduction in liver enzymes and protection from most causes of cirrhosis. Using an exome-wide ... ...

Abstract	Recent human genome-wide association studies have identified common missense variants in MARC1, p.Ala165Thr and p.Met187Lys, associated with lower hepatic fat, reduction in liver enzymes and protection from most causes of cirrhosis. Using an exome-wide association study we recapitulated earlier MARC1 p.Ala165Thr and p.Met187Lys findings in 540,000 individuals from five ancestry groups. We also discovered novel rare putative loss of function variants in MARC1 with a phenotype similar to MARC1 p.Ala165Thr/p.Met187Lys variants. In vitro studies of recombinant human MARC1 protein revealed Ala165Thr substitution causes protein instability and aberrant localization in hepatic cells, suggesting MARC1 inhibition or deletion may lead to hepatoprotection. Following this hypothesis, we generated Marc1 knockout mice and evaluated the effect of Marc1 deletion on liver phenotype. Unexpectedly, our study found that whole-body Marc1 deficiency in mouse is not protective against hepatic triglyceride accumulation, liver inflammation or fibrosis. In attempts to explain the lack of the observed phenotype, we discovered that Marc1 plays only a minor role in mouse liver while its paralogue Marc2 is the main Marc family enzyme in mice. Our findings highlight the major difference in MARC1 physiological function between human and mouse.
MeSH term(s)	Animals ; Humans ; Mice ; Genome-Wide Association Study ; Liver Cirrhosis ; Oximes
Chemical Substances	amidoxime ; Oximes ; mitochondrial amidoxime reducing component 1, human (EC 1.-)
Language	English
Publishing date	2024-03-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1011179
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Article: An Erythropoietin-Independent Mechanism of Erythrocytic Precursor Proliferation Underlies Hypoxia Tolerance in Sea Nomads.

Ilardo, Melissa / Dos Santos, Maria C Ferreira / Grote Beverborg, Niels / Rajan, Malini / Said, M Abdullah / Verweij, Niek / Van Der Harst, Pim / Van Der Meer, Peter / Leibold, Elizabeth A

Frontiers in physiology

2022 Volume 12, Page(s) 760851

Abstract: The Bajau Sea Nomads were recently demonstrated to have evolved larger spleens as an adaptation to millennia of a marine foraging lifestyle. The large-spleen phenotype appears to derive from increases in thyroid hormone (TH) production as a result of ... ...

Abstract	The Bajau Sea Nomads were recently demonstrated to have evolved larger spleens as an adaptation to millennia of a marine foraging lifestyle. The large-spleen phenotype appears to derive from increases in thyroid hormone (TH) production as a result of reduced expression of phosphodiesterase 10A (PDE10A), though the exact mechanism remains unknown. Through pharmacological inhibition of PDE10A using the selective inhibitor MP-10 in mice, we were able to mimic the Bajau adaptation and show that treated mice had significantly larger spleens than control animals. This difference appears connected to an excess of early stage erythrocytes and an apparent increase in red blood cell (RBC) precursor proliferation in response to increased TH. However, we determined that the stimulation of RBC production in the mouse model
Language	English
Publishing date	2022-01-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564217-0
ISSN	1664-042X
ISSN	1664-042X
DOI	10.3389/fphys.2021.760851
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Article ; Online: Genetically Determined High Levels of Iron Parameters Are Protective for Coronary Artery Disease.

Grote Beverborg, Niels / Said, M Abdullah / van der Wal, Haye H / Verweij, Niek / van der Meer, Peter / van der Harst, Pim

Circulation. Genomic and precision medicine

2020 Volume 13, Issue 1, Page(s) e002544

MeSH term(s)	Aged ; Biomarkers/metabolism ; Coronary Artery Disease/blood ; Coronary Artery Disease/diagnosis ; Coronary Artery Disease/genetics ; Coronary Artery Disease/prevention & control ; Female ; Humans ; Iron/blood ; Male ; Mendelian Randomization Analysis ; Polymorphism, Single Nucleotide ; Predictive Value of Tests
Chemical Substances	Biomarkers ; Iron (E1UOL152H7)
Language	English
Publishing date	2020-01-12
Publishing country	United States
Document type	Letter
ISSN	2574-8300
ISSN (online)	2574-8300
DOI	10.1161/CIRCGEN.119.002544
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Article ; Online: Human genetic determinants of the gut microbiome and their associations with health and disease: a phenome-wide association study.

Groot, Hilde E / van de Vegte, Yordi J / Verweij, Niek / Lipsic, Erik / Karper, Jacco C / van der Harst, Pim

Scientific reports

2020 Volume 10, Issue 1, Page(s) 14771

Abstract: Small-scale studies have suggested a link between the human gut microbiome and highly prevalent diseases. However, the extent to which the human gut microbiome can be considered a determinant of disease and healthy aging remains unknown. We aimed to ... ...

Abstract	Small-scale studies have suggested a link between the human gut microbiome and highly prevalent diseases. However, the extent to which the human gut microbiome can be considered a determinant of disease and healthy aging remains unknown. We aimed to determine the spectrum of diseases that are linked to the human gut microbiome through the utilization of its genetic determinants as a proxy for its composition. 180 single nucleotide polymorphisms (SNPs) known to influence the human gut microbiome were used to assess the association with health and disease outcomes in 422,417 UK Biobank participants. Potential causal estimates were obtained using a Mendelian randomization (MR) approach. From the total sample analysed (mean age was 57 ± 8 years), 194,567 (46%) subjects were male. Median exposure was 66-person years (interquartile range 59-72). Eleven SNPs were significantly associated with 28 outcomes (Bonferroni corrected P value < 4.63·10
MeSH term(s)	Aged ; Case-Control Studies ; Disease/genetics ; Female ; Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; Humans ; Male ; Mendelian Randomization Analysis ; Middle Aged ; Phenomics ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2020-09-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-70724-5
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Article ; Online: Genome-wide association studies and Mendelian randomization analyses for leisure sedentary behaviours.

van de Vegte, Yordi J / Said, M Abdullah / Rienstra, Michiel / van der Harst, Pim / Verweij, Niek

Nature communications

2020 Volume 11, Issue 1, Page(s) 1770

Abstract: Leisure sedentary behaviours are associated with increased risk of cardiovascular disease, but whether this relationship is causal is unknown. The aim of this study is to identify genetic determinants associated with leisure sedentary behaviours and to ... ...

Abstract	Leisure sedentary behaviours are associated with increased risk of cardiovascular disease, but whether this relationship is causal is unknown. The aim of this study is to identify genetic determinants associated with leisure sedentary behaviours and to estimate the potential causal effect on coronary artery disease (CAD). Genome wide association analyses of leisure television watching, leisure computer use and driving behaviour in the UK Biobank identify 145, 36 and 4 genetic loci (P < 1×10
MeSH term(s)	Adult ; Aged ; Body Mass Index ; Coronary Artery Disease/complications ; Coronary Artery Disease/etiology ; Female ; Genome-Wide Association Study ; Humans ; Male ; Mendelian Randomization Analysis ; Mental Disorders/complications ; Mental Disorders/genetics ; Middle Aged ; Risk Factors ; Sedentary Behavior ; United Kingdom/epidemiology
Language	English
Publishing date	2020-04-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-15553-w
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Article: Genetics and the heart rate response to exercise

van de Vegte, Yordi J / Tegegne, Balewgizie S / Verweij, Niek / Snieder, Harold / van der Harst, Pim

Cellular and molecular life sciences. 2019 June, v. 76, no. 12

2019

Abstract: The acute heart rate response to exercise, i.e., heart rate increase during and heart rate recovery after exercise, has often been associated with all-cause and cardiovascular mortality. The long-term response of heart rate to exercise results in ... ...

Abstract	The acute heart rate response to exercise, i.e., heart rate increase during and heart rate recovery after exercise, has often been associated with all-cause and cardiovascular mortality. The long-term response of heart rate to exercise results in favourable changes in chronotropic function, including decreased resting and submaximal heart rate as well as increased heart rate recovery. Both the acute and long-term heart rate response to exercise have been shown to be heritable. Advances in genetic analysis enable researchers to investigate this hereditary component to gain insights in possible molecular mechanisms underlying interindividual differences in the heart rate response to exercise. In this review, we comprehensively searched candidate gene, linkage, and genome-wide association studies that investigated the heart rate response to exercise. A total of ten genes were associated with the acute heart rate response to exercise in candidate gene studies. Only one gene (CHRM2), related to heart rate recovery, was replicated in recent genome-wide association studies (GWASs). Additional 17 candidate causal genes were identified for heart rate increase and 26 for heart rate recovery in these GWASs. Nine of these genes were associated with both acute increase and recovery of the heart rate during exercise. These genes can be broadly categorized into four categories: (1) development of the nervous system (CCDC141, PAX2, SOX5, and CAV2); (2) prolongation of neuronal life span (SYT10); (3) cardiac development (RNF220 and MCTP2); (4) cardiac rhythm (SCN10A and RGS6). Additional 10 genes were linked to long-term modification of the heart rate response to exercise, nine with heart rate increase and one with heart rate recovery. Follow-up will be essential to get functional insights in how candidate causal genes affect the heart rate response to exercise. Future work will be required to translate these findings to preventive and therapeutic applications.
Keywords	exercise ; genes ; genetic analysis ; genome-wide association study ; heart rate ; longevity ; mortality ; neurons ; therapeutics
Language	English
Dates of publication	2019-06
Size	p. 2391-2409.
Publishing place	Springer International Publishing
Document type	Article
Note	Review
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-019-03079-4
Database	NAL-Catalogue (AGRICOLA)

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