scholarly journals Genome-wide association and Mendelian randomization analysis prioritizes bioactive metabolites with putative causal effects on common diseases

Author(s):  
Youwen Qin ◽  
Guillaume Meric ◽  
Tao Long ◽  
Jeramie Watrous ◽  
Stephen Burgess ◽  
...  

Bioactive metabolites are central to numerous pathways and disease pathophysiology, yet many bioactive metabolites are still uncharacterized. Here, we quantified bioactive metabolites using untargeted LC-MS plasma metabolomics in two large cohorts (combined N≈9,300) and utilized genome-wide association analysis and Mendelian randomization to uncover genetic loci with roles in bioactive metabolism and prioritize metabolite features for more in-depth characterization. We identified 118 loci associated with levels of 2,319 distinct metabolite features which replicated across cohorts and reached study-wide significance in meta-analysis. Of these loci, 39 were previously not known to be associated with blood metabolites. Loci harboring SLCO1B1 and UGT1A were highly pleiotropic, accounting for >40% of all associations. Two-sample Mendelian randomization found 46 causal effects of 31 metabolite features on at least one of five common diseases. Of these, 15, including leukotriene D4, had protective effects on both coronary heart disease and primary sclerosing cholangitis. We further assessed the association between baseline metabolite features and incident coronary heart disease using 16 years of follow-up health records. This study characterizes the genetic landscape of bioactive metabolite features and their putative causal effects on disease.

2018 ◽  
Author(s):  
Cavin K. Ward-Caviness ◽  
Paul S. de Vries ◽  
Kerri L. Wiggins, MS ◽  
Jennifer E. Huffman ◽  
Jennifer E. Huffman ◽  
...  

AbstractBackgroundFibrinogen is an essential hemostatic factor and cardiovascular disease risk factor. Early attempts at evaluating the causal effect of fibrinogen on coronary heart disease (CHD) and myocardial infraction (MI) using Mendelian randomization (MR) used single variant approaches, and did not take advantage of recent genome-wide association studies (GWAS) or multi-variant, pleiotropy robust MR methodologies.Methods and FindingsWe evaluated evidence for a causal effect of fibrinogen on both CHD and MI using MR. We used both an allele score approach and pleiotropy robust MR models. The allele score was composed of 38 fibrinogen-associated variants from recent GWAS. Initial analyses using the allele score incorporated data from 11 European-ancestry prospective cohorts to examine incidence CHD and MI. We also applied 2 sample MR methods with data from a prevalent CHD and MI GWAS. Results are given in terms of the hazard ratio (HR) or odds ratio (OR), depending on the study design, and associated 95% confidence interval (CI).In single variant analyses no causal effect of fibrinogen on CHD or MI was observed. In multi-variant analyses using incidence CHD cases and the allele score approach, the estimated causal effect (HR) of a 1 g/L higher fibrinogen concentration was 1.62 (CI = 1.12, 2.36) when using incident cases and the allele score approach. In 2 sample MR analyses that accounted for pleiotropy, the causal estimate (OR) was reduced to 1.18 (CI = 0.98, 1.42) and 1.09 (CI = 0.89, 1.33) in the 2 most precise (smallest CI) models, out of 4 models evaluated. In the 2 sample MR analyses for MI, there was only very weak evidence of a causal effect in only 1 out of 4 models.ConclusionsA small causal effect of fibrinogen on CHD is observed using multi-variant MR approaches which account for pleiotropy, but not single variant MR approaches. Taken together, results indicate that even with large sample sizes and multi-variant approaches MR analyses still cannot exclude the null when estimating the causal effect of fibrinogen on CHD, but that any potential causal effect is likely to be much smaller than observed in epidemiological studies.Author SummaryInitial Mendelian Randomization (MR) analyses of the causal effect of fibrinogen on coronary heart disease (CHD) utilized single variants and did not take advantage of modern, multivariant approaches. This manuscript provides an important update to these initial analyses by incorporating larger sample sizes and employing multiple, modern multi-variant MR approaches to account for pleiotropy. We used incident cases to perform a MR study of the causal effect of fibrinogen on incident CHD and the nested outcome of myocardial infarction (MI) using an allele score approach. Then using data from a case-control genome-wide association study for CHD and MI we performed two sample MR analyses with multiple, pleiotropy robust approaches. Overall, the results indicated that associations between fibrinogen and CHD in observational studies are likely upwardly biased from any underlying causal effect. Single variant MR approaches show little evidence of a causal effect of fibrinogen on CHD or MI. Multi-variant MR analyses of fibrinogen on CHD indicate there may be a small positive effect, however this result needs to be interpreted carefully as the 95% confidence intervals were still consistent with a null effect. Multi-variant MR approaches did not suggest evidence of even a small causal effect of fibrinogen on MI.


2019 ◽  
pp. 204748731989467 ◽  
Author(s):  
Liu Miao ◽  
Guo-Xiong Deng ◽  
Rui-Xing Yin ◽  
Rong-Jun Nie ◽  
Shuo Yang ◽  
...  

Background Although many observational studies have shown an association between plasma homocysteine levels and cardiovascular diseases, controversy remains. In this study, we estimated the role of increased plasma homocysteine levels on the etiology of coronary heart disease and acute myocardial infarction. Methods A two-sample Mendelian randomization study on disease was conducted, i.e. “coronary heart disease” ( n = 184,305) and “acute myocardial infarction” ( n = 181,875). Nine single nucleotide polymorphisms, which were genome-wide significantly associated with plasma homocysteine levels in 57,644 subjects from the Coronary ARtery DIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) plus The Coronary Artery Disease (C4D) Genetics (CARDIoGRAMplusC4D) consortium genome-wide association study and were known to be associated at p < 5×10–8, were used as an instrumental variable. Results None of the nine single nucleotide polymorphisms were associated with coronary heart disease or acute myocardial infarction ( p > 0.05 for all). Mendelian randomization analysis revealed no causal effects of plasma homocysteine levels, either on coronary heart disease (inverse variance weighted; odds ratio = 1.015, 95% confidence interval = 0.923–1.106, p = 0.752) or on acute myocardial infarction (inverse variance weighted; odds ratio = 1.037, 95% confidence interval = 0.932–1.142, p = 0.499). The results were consistent in sensitivity analyses using the weighted median and Mendelian randomization-Egger methods, and no directional pleiotropy ( p = 0.213 for coronary heart disease and p = 0.343 for acute myocardial infarction) was observed. Sensitivity analyses confirmed that plasma homocysteine levels were not significantly associated with coronary heart disease or acute myocardial infarction. Conclusions The findings from this Mendelian randomization study indicate no causal relationship between plasma homocysteine levels and coronary heart disease or acute myocardial infarction. Conflicting findings from observational studies might have resulted from residual confounding or reverse causation.


PLoS Genetics ◽  
2011 ◽  
Vol 7 (2) ◽  
pp. e1001300 ◽  
Author(s):  
Guillaume Lettre ◽  
Cameron D. Palmer ◽  
Taylor Young ◽  
Kenechi G. Ejebe ◽  
Hooman Allayee ◽  
...  

PLoS ONE ◽  
2019 ◽  
Vol 14 (5) ◽  
pp. e0216222 ◽  
Author(s):  
Cavin K. Ward-Caviness ◽  
Paul S. de Vries ◽  
Kerri L. Wiggins ◽  
Jennifer E. Huffman ◽  
Lisa R. Yanek ◽  
...  

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