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Boomsma, D. I.

Publications and source records attributed to Boomsma, D. I..

40 records · Page 3Linked to original sources

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↗

Multivariate Genome-Wide and Integrated Transcriptome and Epigenome-Wide Analyses of the Well-being Spectrum.

Phenotypes related to well-being (life satisfaction, positive affect, neuroticism, and depressive symptoms), are genetically highly correlated (| rg | > .75). Multivariate genome-wide analyses (Nobs = 958,149) of these traits, collectively referred to as the well-being spectrum, reveals 63 significant independent signals, of which 29 were not previously identified. Transcriptome and epigenome analyses implicate variation in gene expression at 8 additional loci and CpG methylation at 6 additional loci in the etiology of well-being. We leverage an anatomically comprehensive survey of gene expression in the brain to annotate our findings, showing that SNPs within genes excessively expressed in the cortex and part of the hippocampal formation are enriched in their effect on well-being.

genetics↗

Stratified Linkage Disequilibrium Score Regression reveals enrichment of eQTL effects on complex traits is not tissue specific

Both gene expression levels and eQTLs (expression quantitative trait loci) are partially tissue-specific, complicating the detection of eQTLs in tissues with limited sample availability, such as the brain. However, eQTL overlap between tissues might be non-trivial, allowing for inference of eQTL functioning in the brain via eQTLs measured in readily accessible tissues, e.g. whole blood. Using Stratified Linkage Disequilibrium Score Regression (SLDSR), we quantify the enrichment in GWAS signal of blood and brain eQTLs in genome-wide association study (GWAS) on 11 complex traits (schizophrenia, BMI, educational attainment, Crohns disease, rheumatoid arthritis, ulcerative colitis, age at menarche, coronary artery disease, height, LDL levels, and smoking behavior). Our analyses established significant enrichment of blood and brain eQTLs in their effects across all traits. As we do not know the true number of causal eQTLs, it is difficult to determine the precise magnitude of enrichment. We found no evidence for tissue-specific enrichment in GWAS signal for either eQTLs uniquely seen in the brain or whole blood. To follow up on our findings, we tested tissue-specific enrichment of eQTLs discovered in 44 tissues by the Genotype-Tissue Expression (GTEx) consortium, and, again, found no tissue-specific eQTL effects. We further integrated the GTEx eQTLs with SNPs associated with tissue-specific histone modifiers, and interrogate its effect on rheumatoid arthritis and schizophrenia. We observed substantially enriched effects on schizophrenia, though again not tissue-specific. Finally, we extracted eQTLs in tissue-specific differentially expressed genes, and determined their effects on rheumatoid arthritis and schizophrenia. We conclude that, while eQTLs are strongly enriched in GWAS signal, the enrichment is not specific to the tissue used in eQTL discovery. Therefore, working with relatively accessible tissues, such as whole blood, as proxy for eQTL discovery is sensible; and restricting lookups for GWAS hits to a specific tissue might not be advisable.

genomics↗

Genome-wide meta-analysis of cognitive empathy: heritability, and correlates with sex, neuropsychiatric conditions and brain anatomy

We conducted a genome-wide meta-analysis of cognitive empathy using the Reading the Mind in the Eyes Test (Eyes Test) in 88,056 research volunteers of European Ancestry (44,574 females and 43,482 males) from 23andMe Inc., and an additional 1,497 research volunteers of European Ancestry (891 females and 606 males) from the Brisbane Longitudinal Twin Study (BLTS). We confirmed a female advantage on the Eyes Test (Cohens d = 0.21, P < 2.2x10-16), and identified a locus in 3p26.1 that is associated with scores on the Eyes Test in females (rs7641347, Pmeta = 1.58 x 10-8). Common single nucleotide polymorphisms (SNPs) explained 5.8% (95% CI: 0.45 - 0.72; P = 1.00 x 10-17) of the total trait variance in both sexes, and we identified a twin heritability of 0.28 (95% CI: 0.13-0.42). Finally, we identified significant genetic correlation between the Eyes Test and anorexia nervosa, measures of empathy (the Empathy Quotient), openness (NEO-Five Factor Inventory), and different measures of educational attainment and cognitive aptitude, and show that the genetic determinants of volumes of the dorsal striatum (caudate nucleus and putamen) are positively correlated with the genetic determinants of performance on the Eyes Test.

genetics↗