Biology subjects

de Geus, E.

Publications and source records attributed to de Geus, E..

4 recordsLinked to original sources

bioRxiv2023

Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

Both gene methylation and the gut microbiome are partially determined by host genetics and partially by environment. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbiome composition using data generated by shotgun metagenomic sequencing (n = 683). We then investigated if genetic and environmental factors can explain the methylation-microbiota associations in a set of 78 associated CpG-taxa pairs from the EWAS meta-analysis. In both cohorts, blood and stool samples were collected within 2 weeks of each other. Methylation was profiled in blood samples using the Illumina 450K array. Methylation and microbiome analysis pipelines were harmonized across cohorts. Epigenome-wide association study (EWAS) of microbial features were analysed using linear regression with adjustment for technical covariates. Discovery and replication analysis using 16s data identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 x 10-11) and cg12234533 (Pmeta-analysis = 4.29 x 10-10). While we did not find human genetic variants that could explain the associated CpG-taxa/pathway pairs, we show that microbiome can mediate the effect of environmental factors on epigenetics. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome.

genomics↗

bioRxiv2020

Genetic analyses identify widespread sex-differential participation bias

Genetic association results are often interpreted with the assumption that study participation does not affect downstream analyses. Understanding the genetic basis of this participation bias is challenging as it requires the genotypes of unseen individuals. However, we demonstrate that it is possible to estimate comparative biases by performing GWAS contrasting one subgroup versus another. For example, we show that sex exhibits autosomal heritability in the presence of sex-differential participation bias. By performing a GWAS of sex in ~3.3 million males and females, we identify over 158 autosomal loci significantly associated with sex and highlight complex traits underpinning differences in study participation between sexes. For example, the body mass index (BMI) increasing allele at the FTO locus was observed at higher frequency in males compared to females (OR 1.02 [1.02-1.03], P=4.4x10-36). Finally, we demonstrate how these biases can potentially lead to incorrect inferences in downstream analyses and propose a conceptual framework for addressing such biases. Our findings highlight a new challenge that genetic studies may face as sample sizes continue to grow.

genetics↗

bioRxiv2018

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo, image-based, large-scale genetic screen in zebrafish

A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5 days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25{micro}M ivabradine - an open channel blocker of HCNs - for 24h resulted in a dose-dependent higher HRV and lower heart rate at 5 days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).

genomics↗

bioRxiv2017

Extending Causality Tests With Genetic Instruments: An Integration Of Mendelian Randomization And The Classical Twin Design

Mendelian Randomization (MR) is an important approach to modelling causality in non-experimental settings. MR uses genetic instruments to test causal relationships between exposures and outcomes of interest. Individual genetic variants have small effects, and so, when used as instruments, render MR liable to weak instrument bias. Polygenic scores have the advantage of larger effects, but may be characterized by direct pleiotropy, which violates a central assumption of MR.\n\nWe developed the MR-DoC twin model by integrating MR with the Direction of Causation twin model. This model allows us to test pleiotropy directly. We considered the issue of parameter identification, and given identification, we conducted extensive power calculations. MR-DoC allows one to test causal hypotheses and to obtain unbiased estimates of the causal effect given pleiotropic instruments (polygenic scores), while controlling for genetic and environmental influences common to the outcome and exposure. Furthermore, MR-DoC in twins has appreciably greater statistical power than a standard MR analysis applied to singletons, if the unshared environmental effects on the exposure and the outcome are uncorrelated. Generally, power increases with: 1) decreasing residual exposure-outcome correlation, and 2) decreasing heritability of the exposure variable.\n\nMR-DoC allows one to employ strong instrumental variables (polygenic scores, possibly pleiotropic), guarding against weak instrument bias and increasing the power to detect causal effects. Our approach will enhance and extend MRs range of applications, and increase the value of the large cohorts collected at twin registries as they correctly detect causation and estimate effect sizes even in the presence of pleiotropy.

genetics↗