Shared genetic factors do not account for the observed co-occurrence of depression and autoimmune diseases in the UK Biobank

AbstractBackgroundEpidemiological studies have shown increased comorbidity between depression and autoimmune diseases. The mechanisms driving the comorbidity are poorly understood, and a highly powered investigation is needed to understand the relative importance of shared genetic influences. We investigated the evidence for pleiotropy from shared genetic risk alleles between these traits in the UK Biobank (UKB).MethodsWe defined autoimmune and depression cases using information from hospital episode statistics, self-reported conditions and medications, and mental health questionnaires. Pairwise comparisons of depression prevalence between autoimmune cases and controls, and vice-versa, were performed. Cross-trait polygenic risk score (PRS) analyses were performed to test for pleiotropy, i.e. testing whether PRS for depression could predict autoimmune disease status, and vice-versa.ResultsWe identified 28k cases of autoimmune diseases (pooling across 14 traits), and 65k cases of depression. The prevalence of depression was significantly higher in autoimmune cases compared to controls, and vice-versa. PRS for myasthenia gravis and psoriasis were significantly associated with depression case-status (p < 5.2×10−5, R2 <= 0.04%). PRS for depression were significantly associated with case-status for coeliac disease, inflammatory bowel disease, psoriasis, psoriatic arthritis, rheumatoid arthritis and type 1 diabetes (p < 5.8×10−5, R2 range 0.06% to 0.27%).ConclusionsConsistent with the literature, depression was more common in individuals with autoimmune diseases compared to controls, and vice-versa, in the UKB. PRS showed some evidence for involvement of shared genetic factors, but the modest R2 values suggest that shared genetic architecture accounts for only a small proportion of the increased risk across traits.

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Abstract P147: Genome Wide Assessment of Shared Genetic Architecture Between Rheumatoid Arthritis and Cardiovascular Diseases Using the UK Biobank Data

Circulation ◽

10.1161/circ.141.suppl_1.p147 ◽

2020 ◽

Vol 141 (Suppl_1) ◽

Author(s):

Yanjun Guo ◽

Wonil Chung ◽

Zhilei Shan ◽

Liming Liang

Keyword(s):

Cardiovascular Diseases ◽

Genetic Correlation ◽

Multiple Testing ◽

Mendelian Randomization ◽

Meta Analysis ◽

Uk Biobank ◽

Increased Risk ◽

The Uk ◽

Cardiovascular Traits ◽

Shared Genetic

Background: Patients with RA have a 2-10 folds increased risk of cardiovascular diseases (CVD) and CVD accounts for almost 50% of the excess mortality in patients with RA when compared with general population, but the mechanisms underlying such associations are largely unknown. Methods: We examined the genetic correlation, causality, and shared genetic variants between RA (Ncase=6,756, Ncontrol=452,476) and CVD (Ncase=44,246, Ncontrol=414,986) using LD Score regression (LDSC), generalized summary-data-based Mendelian Randomization (GSMR), and cross-trait meta-analysis in the UK Biobank Data. Results: In the present study, RA was significantly genetically correlated with MI, angina, CHD, and CVD after correcting for multiple testing (Rg ranges from 0.40 to 0.43, P<0.05/5). Interestingly, when stratified by frequent usage of aspirin and paracetamol, we observed increased genetic correlation between RA and CVD for participants without aspirin usage ( Rg increased to 0.54 [95%CI: 0.54, 0.78] for angina; P value=6.69х10 -6 ), and for participants with usage of paracetamol ( Rg increased to 0.75 [95%CI: 0.20, 1.29] for MI; P value=8.90х10 -3 ). Cross-trait meta-analysis identified 9 independent loci that were shared between RA and at least one of the genetically correlated CVD traits including PTPN22 at chr1p13.2 , BCL2L11 at chr2q13 , and CCR3 at chr3p21.31 ( P single trait <1х10 -3 and P meta <5х10 -8 ) highlighting potential shared etiology between them which include accelerating atherosclerosis and upregulating oxidative stress and vascular permeability. Finally, Mendelian randomization analyses observed inconsistent instrumental effects and were unable to conclude the causality and directionality between RA and CVD. Conclusion: Our results supported positive genetic correlation between RA and multiple cardiovascular traits, and frequent usage of aspirin and paracetamol may modify their associations, but instrumental analyses were unable to conclude the causality and directionality between them.

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Polygenic Risk Score Prediction for Endometriosis

Frontiers in Reproductive Health ◽

10.3389/frph.2021.793226 ◽

2021 ◽

Vol 3 ◽

Author(s):

Kirstine Kloeve-Mogensen ◽

Palle Duun Rohde ◽

Simone Twisttmann ◽

Marianne Nygaard ◽

Kristina Magaard Koldby ◽

...

Keyword(s):

Risk Score ◽

Genome Wide Association Study ◽

Polygenic Risk Score ◽

Uk Biobank ◽

Standard Deviation Increase ◽

Polygenic Risk ◽

Clinical Risk ◽

Risk Variants ◽

Increased Risk ◽

The Uk

Endometriosis is a major health care challenge because many young women with endometriosis go undetected for an extended period, which may lead to pain sensitization. Clinical tools to better identify candidates for laparoscopy-guided diagnosis are urgently needed. Since endometriosis has a strong genetic component, there is a growing interest in using genetics as part of the clinical risk assessment. The aim of this work was to investigate the discriminative ability of a polygenic risk score (PRS) for endometriosis using three different cohorts: surgically confirmed cases from the Western Danish endometriosis referral Center (249 cases, 348 controls), cases identified from the Danish Twin Registry (DTR) based on ICD-10 codes from the National Patient Registry (140 cases, 316 controls), and replication analysis in the UK Biobank (2,967 cases, 256,222 controls). Patients with adenomyosis from the DTR (25 cases) and from the UK Biobank (1,883 cases) were included for comparison. The PRS was derived from 14 genetic variants identified in a published genome-wide association study with more than 17,000 cases. The PRS was associated with endometriosis in surgically confirmed cases [odds ratio (OR) = 1.59, p = 2.57× 10−7] and in cases from the DTR biobank (OR = 1.50, p = 0.0001). Combining the two Danish cohorts, each standard deviation increase in PRS was associated with endometriosis (OR = 1.57, p = 2.5× 10−11), as well as the major subtypes of endometriosis; ovarian (OR = 1.72, p = 6.7× 10−5), infiltrating (OR = 1.66, p = 2.7× 10−9), and peritoneal (OR = 1.51, p = 2.6 × 10−3). These findings were replicated in the UK Biobank with a much larger sample size (OR = 1.28, p < 2.2× 10−16). The PRS was not associated with adenomyosis, suggesting that adenomyosis is not driven by the same genetic risk variants as endometriosis. Our results suggest that a PRS captures an increased risk of all types of endometriosis rather than an increased risk for endometriosis in specific locations. Although the discriminative accuracy is not yet sufficient as a stand-alone clinical utility, our data demonstrate that genetics risk variants in form of a simple PRS may add significant new discriminatory value. We suggest that an endometriosis PRS in combination with classical clinical risk factors and symptoms could be an important step in developing an urgently needed endometriosis risk stratification tool.

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Genetically determined risk of keratinocyte carcinoma and risk of other cancers

International Journal of Epidemiology ◽

10.1093/ije/dyaa265 ◽

2020 ◽

Author(s):

Jean Claude Dusingize ◽

Catherine M Olsen ◽

Jiyuan An ◽

Nirmala Pandeya ◽

Upekha E Liyanage ◽

...

Keyword(s):

Genetic Variants ◽

Genome Wide Association Study ◽

Meta Analysis ◽

Epidemiological Studies ◽

Risk Scores ◽

Cancer Site ◽

Uk Biobank ◽

Individual Level ◽

Increased Risk ◽

The Uk

Abstract Background Epidemiological studies have consistently documented an increased risk of developing primary non-cutaneous malignancies among people with a history of keratinocyte carcinoma (KC). However, the mechanisms underlying this association remain unclear. We conducted two separate analyses to test whether genetically predicted KC is related to the risk of developing cancers at other sites. Methods In the first approach (one-sample), we calculated the polygenic risk scores (PRS) for KC using individual-level data in the UK Biobank (n = 394 306) and QSkin cohort (n = 16 896). The association between the KC PRS and each cancer site was assessed using logistic regression. In the secondary (two-sample) approach, we used genome-wide association study (GWAS) summary statistics identified from the most recent GWAS meta-analysis of KC and obtained GWAS data for each cancer site from the UK-Biobank participants only. We used inverse-variance-weighted methods to estimate risks across all genetic variants. Results Using the one-sample approach, we found that the risks of cancer at other sites increased monotonically with KC PRS quartiles, with an odds ratio (OR) of 1.16, 95% confidence interval (CI): 1.13–1.19 for those in KC PRS quartile 4 compared with those in quartile 1. In the two-sample approach, the pooled risk of developing other cancers was statistically significantly elevated, with an OR of 1.05, 95% CI: 1.03–1.07 per doubling in the odds of KC. We observed similar trends of increasing cancer risk with increasing KC PRS in the QSkin cohort. Conclusion Two different genetic approaches provide compelling evidence that an instrumental variable for KC constructed from genetic variants predicts the risk of cancers at other sites.

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Genetic variants are identified to increase risk of COVID-19 related mortality from UK Biobank data

Human Genomics ◽

10.1186/s40246-021-00306-7 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Jianchang Hu ◽

Cai Li ◽

Shiying Wang ◽

Ting Li ◽

Heping Zhang

Keyword(s):

Genetic Variants ◽

Genetic Factors ◽

Genome Wide Association Study ◽

Individual Risk ◽

Uk Biobank ◽

Risk Of Death ◽

Genome Wide ◽

A Genome ◽

Increased Risk ◽

The Uk

Abstract Background The severity of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly heterogeneous. Studies have reported that males and some ethnic groups are at increased risk of death from COVID-19, which implies that individual risk of death might be influenced by host genetic factors. Methods In this project, we consider the mortality as the trait of interest and perform a genome-wide association study (GWAS) of data for 1778 infected cases (445 deaths, 25.03%) distributed by the UK Biobank. Traditional GWAS fails to identify any genome-wide significant genetic variants from this dataset. To enhance the power of GWAS and account for possible multi-loci interactions, we adopt the concept of super variant for the detection of genetic factors. A discovery-validation procedure is used for verifying the potential associations. Results We find 8 super variants that are consistently identified across multiple replications as susceptibility loci for COVID-19 mortality. The identified risk factors on chromosomes 2, 6, 7, 8, 10, 16, and 17 contain genetic variants and genes related to cilia dysfunctions (DNAH7 and CLUAP1), cardiovascular diseases (DES and SPEG), thromboembolic disease (STXBP5), mitochondrial dysfunctions (TOMM7), and innate immune system (WSB1). It is noteworthy that DNAH7 has been reported recently as the most downregulated gene after infecting human bronchial epithelial cells with SARS-CoV-2. Conclusions Eight genetic variants are identified to significantly increase the risk of COVID-19 mortality among the patients with white British ancestry. These findings may provide timely clues and potential directions for better understanding the molecular pathogenesis of COVID-19 and the genetic basis of heterogeneous susceptibility, with potential impact on new therapeutic options.

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Socioeconomic Inequalities and Ethnicity Are Associated with a Positive COVID-19 Test among Cancer Patients in the UK Biobank Cohort

Cancers ◽

10.3390/cancers13071514 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1514

Author(s):

Shing Fung Lee ◽

Maja Nikšić ◽

Bernard Rachet ◽

Maria-Jose Sanchez ◽

Miguel Angel Luque-Fernandez

Keyword(s):

Cancer Patients ◽

Socioeconomic Inequalities ◽

Uk Biobank ◽

Incident Cancer ◽

Increased Risk ◽

Exposure Variable ◽

Independent Risk Factors ◽

The Uk ◽

Deprived Areas

We explored the role of socioeconomic inequalities in COVID-19 incidence among cancer patients during the first wave of the pandemic. We conducted a case-control study within the UK Biobank cohort linked to the COVID-19 tests results available from 16 March 2020 until 23 August 2020. The main exposure variable was socioeconomic status, assessed using the Townsend Deprivation Index. Among 18,917 participants with an incident malignancy in the UK Biobank cohort, 89 tested positive for COVID-19. The overall COVID-19 incidence was 4.7 cases per 1000 incident cancer patients (95%CI 3.8–5.8). Compared with the least deprived cancer patients, those living in the most deprived areas had an almost three times higher risk of testing positive (RR 2.6, 95%CI 1.1–5.8). Other independent risk factors were ethnic minority background, obesity, unemployment, smoking, and being diagnosed with a haematological cancer for less than five years. A consistent pattern of socioeconomic inequalities in COVID-19 among incident cancer patients in the UK highlights the need to prioritise the cancer patients living in the most deprived areas in vaccination planning. This socio-demographic profiling of vulnerable cancer patients at increased risk of infection can inform prevention strategies and policy improvements for the coming pandemic waves.

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Polygenic risk for schizophrenia and season of birth within the UK Biobank cohort

Psychological Medicine ◽

10.1017/s0033291718000454 ◽

2018 ◽

Vol 49 (15) ◽

pp. 2499-2504 ◽

Cited By ~ 7

Author(s):

Valentina Escott-Price ◽

Daniel J. Smith ◽

Kimberley Kendall ◽

Joey Ward ◽

George Kirov ◽

...

Keyword(s):

Environmental Exposure ◽

Copy Number Variants ◽

Season Of Birth ◽

Uk Biobank ◽

Month Of Birth ◽

Risk Alleles ◽

Gene Environment ◽

Increased Risk ◽

The Uk ◽

Pathogenic Process

AbstractBackgroundThere is strong evidence that people born in winter and in spring have a small increased risk of schizophrenia. As this ‘season of birth’ effect underpins some of the most influential hypotheses concerning potentially modifiable risk exposures, it is important to exclude other possible explanations for the phenomenon.MethodsHere we sought to determine whether the season of birth effect reflects gene-environment confounding rather than a pathogenic process indexing environmental exposure. We directly measured, in 136 538 participants from the UK Biobank (UKBB), the burdens of common schizophrenia risk alleles and of copy number variants known to increase the risk for the disorder, and tested whether these were correlated with a season of birth.ResultsNeither genetic measure was associated with season or month of birth within the UKBB sample.ConclusionsAs our study was highly powered to detect small effects, we conclude that the season of birth effect in schizophrenia reflects a true pathogenic effect of environmental exposure.

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Accuracy of Electronic Health Record Data for Identifying Stroke Cases in Large-Scale Epidemiological Studies: A Systematic Review from the UK Biobank Stroke Outcomes Group

PLoS ONE ◽

10.1371/journal.pone.0140533 ◽

2015 ◽

Vol 10 (10) ◽

pp. e0140533 ◽

Cited By ~ 39

Author(s):

Rebecca Woodfield ◽

Ian Grant ◽

Cathie L. M. Sudlow ◽

◽

Keyword(s):

Systematic Review ◽

Electronic Health Record ◽

Large Scale ◽

Epidemiological Studies ◽

Health Record ◽

Uk Biobank ◽

Electronic Health Record Data ◽

Stroke Outcomes ◽

Record Data ◽

The Uk

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Associations of cigarette smoking with gray and white matter in the UK Biobank

10.31234/osf.io/wyvnm ◽

2019 ◽

Author(s):

Joshua Gray ◽

Matthew Thompson ◽

Chelsie Benca-Bachman ◽

Max Michael Owens ◽

Mikela Murphy ◽

...

Keyword(s):

White Matter ◽

Cigarette Smoking ◽

Gray Matter ◽

Brain Structure ◽

Mean Diffusivity ◽

Medial Lemniscus ◽

Uk Biobank ◽

Matter Volume ◽

Increased Risk ◽

The Uk

Chronic cigarette smoking is associated with increased risk for myriad health consequences including cognitive decline and dementia, but research on the link between smoking and brain structure is nascent. We assessed the relationship of cigarette smoking (ever smoked, cigarettes per day, and duration) with gray and white matter using the UK Biobank cohort (gray matter N = 19,615; white matter N = 17,760), adjusting for numerous demographic and health confounders. Ever smoked and duration were associated with smaller total gray matter volume. Ever smoked was associated with reduced volume of the right VIIIa cerebellum, as well as elevated white matter hyperintensity volumes. Smoking duration was associated with reduced total white matter volume. With regard to specific tracts, ever smoked was associated with reduced fractional anisotropy in the left cingulate gyrus part of the cingulum, left posterior thalamic radiation, and bilateral superior thalamic radiation and increased mean diffusivity in the middle cerebellar peduncle, right medial lemniscus, bilateral posterior thalamic radiation, and bilateral superior thalamic radiation. Overall, we found significant associations of cigarette exposure with global measures of gray and white matter. Furthermore, we found select associations of ever smoked, but not cigarettes per day or duration, with specific gray and white matter regions. These findings inform our understanding of the connections between smoking and variation in brain structure and clarify potential mechanisms of risk for common neurological sequelae.

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Diabetes, glycated haemoglobin and the risk of myocardial infarction in women and men: a prospective cohort study of the UK Biobank

10.2337/figshare.12302741.v1 ◽

2020 ◽

Author(s):

Marit de Jong ◽

Mark Woodward ◽

Sanne A.E Peters

Keyword(s):

Myocardial Infarction ◽

Sex Differences ◽

Glycated Haemoglobin ◽

Incidence Rates ◽

Undiagnosed Diabetes ◽

Uk Biobank ◽

Diabetes Status ◽

Increased Risk ◽

The Uk ◽

Diagnosed Diabetes

Objective: Diabetes has shown to be a stronger risk factor for myocardial infarction (MI) in women than men. Whether sex differences exist across the glycaemic spectrum is unknown. We investigated sex differences in the associations of diabetes status and glycated haemoglobin (HbA1c) with the risk of MI. Research Design and Methods: Data were used from 471,399 (56% women) individuals without cardiovascular disease (CVD) included in the UK Biobank. Sex-specific incidence rates were calculated by diabetes status and across levels of HbA1c, using Poisson regression. Cox proportional hazards analyses estimated sex-specific hazard ratios (HR) and women-to-men ratios by diabetes status and HbA1c for MI during a mean follow-up of 9 years. Results: Women had lower incidence rates of MI than men, regardless of diabetes status or HbA1c level. Compared with individuals without diabetes, prediabetes, undiagnosed diabetes, and previously diagnosed diabetes were associated with increased risk of MI in both sexes. Previously diagnosed diabetes was more strongly associated with MI in women (HR 2∙33 [95%CI 1∙96;2∙78]) than men (1∙81 [1∙63;2∙02]), with a women-to-men ratio of HRs of 1∙29 (1∙05;1∙58). Each 1% higher HbA1c, independent of diabetes status, was associated with an 18% greater risk of MI in both women and men. Conclusions: Although the incidence of MI was higher in men than women, the presence of diabetes is associated with a greater excess relative risk of MI in women. However, each 1% higher HbA1c was associated with an 18% greater risk of MI in both women and men.

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