Paul F. O’Reilly

This paper introduces GSR, a method to adjust for pathway overlap in GWAS gene set enrichment, improving the accuracy of identifying biologically relevant pathways.

The paper analyses gene expression of disease-associated genes across 46 tissues and 204 cell types to identify their expression patterns in relation to 11 diseases and cancers.

This study identifies pathway-level polygenicity in anorexia nervosa by constructing pathway-based polygenic risk scores and finding 497 associated pathways.

This paper uses sibling data to infer genetic architecture of extreme trait values, distinguishing between polygenic and rare variant influences.

The paper identifies departures from polygenic architecture in the tails of complex traits, showing rare alleles are more prevalent and impactful in extreme trait values.

This study shows that stabilising selection enriches the tails of complex traits with rare alleles of large effect, which may have significant clinical implications.

The paper introduces trumpet plots to visualize the relationship between allele frequency and effect size in genetic association studies, using UK Biobank data and providing an R package and Shiny app for analysis.

The paper shows that non-additive effects of schizophrenia risk genes are due to convergent downstream transcriptomic effects and sub-additive changes, suggesting functional redundancy as a mechanism for non-additivity.

BridgePRS improves polygenic risk score accuracy in non-European populations by leveraging shared genetic effects across ancestries, outperforming existing methods in simulated and real data.

This study shows that schizophrenia risk genes have convergent and non-additive transcriptomic effects when perturbed together in human neurons, suggesting functional redundancy and complex interactions.

EraSOR addresses sample overlap in polygenic score analyses by adjusting for inflation in PRS prediction and association statistics, improving robustness in the presence of inter-cohort overlap.

This study evaluates the prognostic value of polygenic risk scores for schizophrenia and finds they do not improve outcome prediction beyond clinical features.

The paper quantifies genetic confounding in epidemiological associations between maternal education and child outcomes, showing significant attenuation when adjusting for polygenic scores and heritability estimates.

This study uses multiple depression measures to improve the validity of Major Depressive Disorder cases in the UK Biobank, finding increased genetic contribution with more measures.

This study uses Mendelian randomization to assess causal relationships between 22 risk factors and the Alzheimer's phenome, finding education, blood pressure, cholesterol, smoking, and BMI have causal effects.

Best-practice guidance for polygenic risk score (PRS) analysis: PRS-specific quality control, shrinkage and linkage disequilibrium handling, liability-scale R^2, overfitting control, and UK Biobank power examples.

This study identifies traits associated with polygenic risk for depression using UK Biobank data and finds causal links between depression risk and brain structure, as well as environmental interactions.

The paper examines phenotypic and genetic relationships between cannabis use, depression, and self-harm using UK Biobank and consortium data, finding associations and genetic correlations.

The paper studies 45 common human polymorphic inversions, showing their functional and evolutionary impact, including gene disruption and association with phenotypic traits.

This study compares within- and between-family polygenic score predictions for eight life outcomes in DZ twins, finding that cognitive traits show greater between-family prediction, which is explained by socio-economic status.

This study investigates the genetic and environmental links between major depressive disorder and traumatic experiences using UK Biobank data, finding shared genetic factors and distinct patterns in trauma-exposed individuals.

This study examines the association between schizophrenia polygenic risk scores and 420 behavioural traits in the UK Biobank, identifying potential causal pathways and highlighting the need for further research.

This paper investigates gene-environment correlation by showing that children's genetic predispositions to BMI influence parental feeding practices, with polygenic scores linked to restriction and pressure.

This study applies polygenic risk scores to a single cohort to identify shared genetic aetiology across hundreds of traits, revealing pleiotropy and novel genetic associations.

This study identifies 6 new blood pressure loci and 48 genes involved in BP regulation using GWAS and gene expression data from blood and kidney tissues.

This study identifies genetic loci associated with early childhood growth phenotypes and links them to later adiposity traits, suggesting potential targets for obesity prevention.