A robust two‐sample transcriptome‐wide Mendelian randomization method integrating GWAS with multi‐tissue eQTL summary statistics

To examine whether psychological traits (PT) had causal effects on Mouth Ulcers (MU), we applied two-sample Mendelian randomization (MR) to genetics association summary statistics of eleven PT and MU. After the adjustment of outlier variants, genetic correlations and multiple testing, well-being (WB) spectrum PT like life satisfactory (odds ratio [OR] = 0.638 per one standard deviation increment of PT score) had protective effects on MU. Reverse WB traits like neuroticism (OR = 1.60) increased the risk of MU. The lack of well-being characteristics may increase the risk of MU, which highlighted the value of preventive oral care for people who have a reverse mental condition.

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Causal Inference Between Chronic Periodontitis and Chronic Kidney Disease: A Bidirectional Mendelian Randomization Analysis in a European Population

Frontiers in Genetics ◽

10.3389/fgene.2021.676136 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jie Yang ◽

Tianyi Chen ◽

Yahong Zhu ◽

Mingxia Bai ◽

Xingang Li

Keyword(s):

Chronic Kidney Disease ◽

Kidney Disease ◽

Causal Inference ◽

Causal Relationship ◽

Instrumental Variables ◽

Chronic Periodontitis ◽

Mendelian Randomization ◽

Association Studies ◽

Genome Wide Association Studies ◽

Summary Statistics

BackgroundPrevious epidemiological studies have shown significant associations between chronic periodontitis (CP) and chronic kidney disease (CKD), but the causal relationship remains uncertain. Aiming to examine the causal relationship between these two diseases, we conducted a bidirectional two-sample Mendelian randomization (MR) analysis with multiple MR methods.MethodsFor the casual effect of CP on CKD, we selected seven single-nucleotide polymorphisms (SNPs) specific to CP as genetic instrumental variables from the genome-wide association studies (GWAS) in the GLIDE Consortium. The summary statistics of complementary kidney function measures, i.e., estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN), were derived from the GWAS in the CKDGen Consortium. For the reversed causal inference, six SNPs associated with eGFR and nine with BUN from the CKDGen Consortium were included and the summary statistics were extracted from the CLIDE Consortium.ResultsNo significant causal association between genetically determined CP and eGFR or BUN was found (all p > 0.05). Based on the conventional inverse variance-weighted method, one of seven instrumental variables supported genetically predicted CP being associated with a higher risk of eGFR (estimate = 0.019, 95% CI: 0.012–0.026, p < 0.001).ConclusionEvidence from our bidirectional causal inference does not support a causal relation between CP and CKD risk and therefore suggests that associations reported by previous observational studies may represent confounding.

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MR-LDP: a two-sample Mendelian randomization for GWAS summary statistics accounting for linkage disequilibrium and horizontal pleiotropy

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqaa028 ◽

2020 ◽

Vol 2 (2) ◽

Cited By ~ 2

Author(s):

Qing Cheng ◽

Yi Yang ◽

Xingjie Shi ◽

Kar-Fu Yeung ◽

Can Yang ◽

...

Keyword(s):

Risk Factors ◽

Linkage Disequilibrium ◽

Genetic Variants ◽

Mendelian Randomization ◽

Association Studies ◽

Alternative Methods ◽

Genome Wide Association Studies ◽

Summary Statistics ◽

Causal Relationships ◽

Disease Outcomes

Abstract The proliferation of genome-wide association studies (GWAS) has prompted the use of two-sample Mendelian randomization (MR) with genetic variants as instrumental variables (IVs) for drawing reliable causal relationships between health risk factors and disease outcomes. However, the unique features of GWAS demand that MR methods account for both linkage disequilibrium (LD) and ubiquitously existing horizontal pleiotropy among complex traits, which is the phenomenon wherein a variant affects the outcome through mechanisms other than exclusively through the exposure. Therefore, statistical methods that fail to consider LD and horizontal pleiotropy can lead to biased estimates and false-positive causal relationships. To overcome these limitations, we proposed a probabilistic model for MR analysis in identifying the causal effects between risk factors and disease outcomes using GWAS summary statistics in the presence of LD and to properly account for horizontal pleiotropy among genetic variants (MR-LDP) and develop a computationally efficient algorithm to make the causal inference. We then conducted comprehensive simulation studies to demonstrate the advantages of MR-LDP over the existing methods. Moreover, we used two real exposure–outcome pairs to validate the results from MR-LDP compared with alternative methods, showing that our method is more efficient in using all-instrumental variants in LD. By further applying MR-LDP to lipid traits and body mass index (BMI) as risk factors for complex diseases, we identified multiple pairs of significant causal relationships, including a protective effect of high-density lipoprotein cholesterol on peripheral vascular disease and a positive causal effect of BMI on hemorrhoids.

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Smoking and COVID-19: A two-sample Mendelian randomization study

10.1101/2021.03.31.21254730 ◽

2021 ◽

Author(s):

Bing-Kun Zheng ◽

Na Li

Keyword(s):

Observational Studies ◽

Mendelian Randomization ◽

Causal Effect ◽

Dose Effect ◽

Genetic Studies ◽

Host Genetics ◽

Causal Risk Factor ◽

Increased Risk ◽

Summary Data ◽

Randomization Method

AbstractEvidence from observational studies suggested that smokers are at increased risk of coronavirus disease 2019 (COVID-19). We aimed to assess the causal effect of smoking on risk for COVID-19 susceptibility and severity using two-sample Mendelian randomization method. Smoking-associated variants were selected as instrument variables from two largest genetic studies. The latest summary data of COVID-19 that shared on Jan 18, 2021 by the COVID-19 Host Genetics Initiative was used. The present Mendelian randomization study provided genetic evidence that smoking was a causal risk factor for COVID-19 susceptibility and severity. In addition, there may be a dose-effect relationship between smoking and COVID-19 severity.

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The impact of lung function on cardiovascular diseases and cardiovascular risk factors: a two sample bi-directional Mendelian randomization study

10.1101/2020.06.01.20118919 ◽

2020 ◽

Author(s):

SL Au Yeung ◽

MC Borges ◽

DA Lawlor ◽

CM Schooling

Keyword(s):

Risk Factors ◽

Type 2 Diabetes ◽

Lung Function ◽

Mendelian Randomization ◽

Sensitivity Analyses ◽

Summary Statistics ◽

The Impact ◽

Genetic Instruments

AbstractBackgroundObservational studies suggested lung function is inversely associated with cardiovascular disease (CVD) although these studies could be susceptible to residual confounding. We conducted a 2 sample Mendelian randomization study using summary statistics from genome wide association studies (GWAS) to clarify the role of lung function in CVD and its risk factors, and conversely the role of CVD in lung function.MethodsWe obtained genetic instruments for forced expiratory volume in 1 second (FEV1) and forced vital capacity (FVC) from publicly available UK Biobank summary statistics (n = 421,986). We applied these genetic instruments for FEV1 (260) and FVC (320) to publicly available GWAS summary statistics for coronary artery disease (CAD) (n = 184,305), stroke and its subtypes (n = 446,696), atrial fibrillation (n = 1,030,836), and heart failure (n = 977,320) and cardiovascular risk factors. Inverse variance weighting was used to assess the impact of lung function on these outcomes. Sensitivity analyses included MR-Egger, weighted median, MR-PRESSO, and multivariable Mendelian randomization. We also conducted bi-directional Mendelian randomization to assess whether CVD affects lung function.ResultsFEV1 and FVC were inversely associated with CAD (odds ratio (OR) per standard deviation (SD) increase, 0.72 (95% confidence interval (CI) 0.63 to 0.82) and 0.70 (95%CI 0.62 to 0.78)), overall stroke (0.87 (95%CI 0.77 to 0.97), 0.90 (0.82 to 1.00)), ischemic stroke (0.87 (95%CI 0.77 to 0.99), 0.90 (95%CI 0.80 to 1.00)), small vessel stroke (0.78, (95%CI 0.61 to 1.00), 0.74 (95%CI 0.61 to 0.92)), and large artery stroke (0.69 (95%CI 0.54 to 0.89), 0.72 (95%CI 0.57 to 0.91)). FEV1 and FVC were inversely associated with type 2 diabetes (0.75 (95%CI 0.62 to 0.90), 0.67 (95%CI 0.58 to 0.79)) and systolic blood pressure. Sensitivity analyses produced similar direction for most outcomes although the magnitude sometimes differed. Adjusting for height attenuated results for CAD (e.g. OR for 1SD FEV1 0.95 (0.76 to 1.20), but this may reflect weak instrument bias. This adjustment did not attenuate effects for stroke or type 2 diabetes. No strong evidence was observed for CVD affecting lung function.ConclusionHigher lung function likely protect against CAD and stroke.

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Mendelian randomization while jointly modeling cis genetics identifies causal relationships between gene expression and lipids

Nature Communications ◽

10.1038/s41467-020-18716-x ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Adriaan van der Graaf ◽

◽

Annique Claringbould ◽

Antoine Rimbert ◽

Harm-Jan Westra ◽

...

Keyword(s):

Gene Expression ◽

Complex Traits ◽

Mendelian Randomization ◽

Low Density Lipoprotein ◽

Density Lipoprotein ◽

Summary Statistics ◽

Low Density Lipoprotein Cholesterol ◽

Causal Inferences ◽

Individual Level ◽

Level Data

Abstract Inference of causality between gene expression and complex traits using Mendelian randomization (MR) is confounded by pleiotropy and linkage disequilibrium (LD) of gene-expression quantitative trait loci (eQTL). Here, we propose an MR method, MR-link, that accounts for unobserved pleiotropy and LD by leveraging information from individual-level data, even when only one eQTL variant is present. In simulations, MR-link shows false-positive rates close to expectation (median 0.05) and high power (up to 0.89), outperforming all other tested MR methods and coloc. Application of MR-link to low-density lipoprotein cholesterol (LDL-C) measurements in 12,449 individuals with expression and protein QTL summary statistics from blood and liver identifies 25 genes causally linked to LDL-C. These include the known SORT1 and ApoE genes as well as PVRL2, located in the APOE locus, for which a causal role in liver was not known. Our results showcase the strength of MR-link for transcriptome-wide causal inferences.

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An iterative approach to detect pleiotropy and perform Mendelian Randomization analysis using GWAS summary statistics

Bioinformatics ◽

10.1093/bioinformatics/btaa985 ◽

2020 ◽

Author(s):

Xiaofeng Zhu ◽

Xiaoyin Li ◽

Rong Xu ◽

Tao Wang

Keyword(s):

Complex Traits ◽

Mendelian Randomization ◽

Causal Effect ◽

Association Studies ◽

Real Data ◽

Supplementary Information ◽

Genome Wide Association Studies ◽

Summary Statistics ◽

Causal Relationships ◽

Multiple Traits

Abstract Motivation The overall association evidence of a genetic variant with multiple traits can be evaluated by cross-phenotype association analysis using summary statistics from genome-wide association studies. Further dissecting the association pathways from a variant to multiple traits is important to understand the biological causal relationships among complex traits. Results Here, we introduce a flexible and computationally efficient Iterative Mendelian Randomization and Pleiotropy (IMRP) approach to simultaneously search for horizontal pleiotropic variants and estimate causal effect. Extensive simulations and real data applications suggest that IMRP has similar or better performance than existing Mendelian Randomization methods for both causal effect estimation and pleiotropic variant detection. The developed pleiotropy test is further extended to detect colocalization for multiple variants at a locus. IMRP will greatly facilitate our understanding of causal relationships underlying complex traits, in particular, when a large number of genetic instrumental variables are used for evaluating multiple traits. Availability and implementation The software IMRP is available at https://github.com/XiaofengZhuCase/IMRP. The simulation codes can be downloaded at http://hal.case.edu/∼xxz10/zhu-web/ under the link: MR Simulations software. Supplementary information Supplementary data are available at Bioinformatics online.

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Herpesvirus Infections and Alzheimer’s Disease: A Mendelian Randomization Study

10.21203/rs.3.rs-323013/v1 ◽

2021 ◽

Author(s):

Shu-Yi Huang ◽

Yu-Xiang Yang ◽

Kevin Kuo ◽

Hong-Qi Li ◽

Xue-Ning Shen ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Family History ◽

Mendelian Randomization ◽

Association Studies ◽

Genome Wide Association Studies ◽

Summary Statistics ◽

Primary Analysis ◽

Varicella Zoster ◽

History Of

Abstract BackgroundObservational studies have suggested that herpesvirus infection increased the risk of Alzheimer’s disease (AD), but it is unclear whether the association is causal. The aim of the present study is to evaluate the causal relationship between four herpesvirus infections and AD. MethodsWe performed a two-sample Mendelian randomization analysis to investigate association of four active herpesvirus infections with AD using summary statistics from genome-wide association studies. The four herpesvirus infections (i.e., chickenpox, shingles, cold sores, mononucleosis) are caused by varicella-zoster virus, herpes simplex virus type 1, and Epstein-Barr virus (EBV), respectively. A large summary statistics data from International Genomics of Alzheimer’s Project was used in primary analysis, including 21,982 AD cases and 41,944 controls. Validation was further performed using family history of AD data from UK Biobank (27,696 cases of maternal AD, 14,338 cases of paternal AD and 272,244 controls).ResultsWe found evidence of a suggestive association between mononucleosis (caused by EBV) and risk of AD (odds ratio [OR] = 1.634, 95% confidence interval [CI] = 1.092-2.446, P = 0.017) after Bonferroni correction. It has been verified in validation analysis that mononucleosis is also associated with family history of AD (OR [95% CI] = 1.392 [1.061, 1.826], P=0.017). Genetically predicted shingles were associated with AD risk (OR [95% CI] = 0.867 [0.784, 0.958], P = 0.005). While genetically predicted chickenpox was suggestively associated with increased family history of AD (OR [95% CI] = 1.147 [1.007, 1.307], P = 0.039).ConclusionsOur findings provided evidence supporting a positive relationship between mononucleosis and AD, indicating a causal link between EBV infection and AD. Further elucidations of this association and underlying mechanisms are likely to identify feasible interventions to promote AD prevention.

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