Peter M. Visscher

From Nagelkerke's R2 to Liability-Scale Variance Explained for Polygenic Scores

This paper provides a new method to directly transform logistic regression results to liability-scale variance explained for polygenic scores, validated by simulation.

Polygenic and familial contributions to antidepressant continuation, switching, discontinuation and augmentation in the All of Us and Pharmlines cohorts

The paper investigates polygenic and familial factors influencing antidepressant treatment outcomes in two cohorts, finding associations between depression polygenic scores and treatment switching, with some links to schizophrenia and bipolar disorder.

Within-family heritability estimates for behavioural and disease phenotypes from 500,000 sibling pairs of diverse ancestries

The paper estimates heritability for behavioural and disease traits using 500,000 sibling pairs across diverse ancestries, finding substantial genetic contributions for smoking, alcohol use, personality, and diseases like T2D and asthma.

Combinatorial effects of gene dosage, polygenic background and environment on complex traits

The paper examines how gene dosage, polygenic background, and environment influence complex traits like height and BMI using large-scale data from multiple cohorts.

Pitfalls in estimating and interpreting the contribution of ultra-rare genetic variants to the heritability of complex traits

The paper identifies biases in estimating heritability from ultra-rare variants and shows that accounting for these biases reveals significant heritability estimates for several traits.

Genome-wide fine-mapping improves identification of causal variants

This paper improves causal variant identification by genome-wide fine-mapping, showing it outperforms existing methods and identifies new causal variants for complex traits.

Joint Bayesian modelling of molecular QTL and GWAS effects improves polygenic prediction for complex traits

Quantifying annotation-stratified pleiotropy and co-polygenicity between complex traits

This paper introduces SBayesAPP, a Bayesian model that estimates annotation-stratified pleiotropy and co-polygenicity between complex traits using GWAS summary statistics, revealing cell-type-specific genetic correlations.

Trans-eQTLs reveal the architecture of human gene regulatory networks

The paper maps cis- and trans-eQTLs in blood samples to infer gene regulatory networks and prioritize trait-relevant pathways.

Multi-ancestry conditional and joint analysis (Manc-COJO) applied to GWAS summary statistics

This paper introduces Manc-COJO, a method for multi-ancestry conditional and joint analysis of GWAS summary statistics, improving detection of independent signals and reducing false positives.

Converging evidence of positive selection at height-associated loci in Europe

The paper reassesses selection on height using GWAS and allele frequency data, finding positive selection at height-associated loci in Europe.

Direct effect of genetic ancestry on complex traits in a Mexican population

The paper estimates direct effects of genetic ancestry on complex traits in a Mexican population using family-based analyses and finds significant associations for height and type 2 diabetes but not for educational attainment.

Transcriptional and translational genetic control in blood contributes significantly to complex trait heritability and polygenic prediction

The paper evaluates the contribution of expression, splicing, and protein QTL in blood to SNP-based heritability and polygenic prediction across 27 traits, finding they capture significant portions of genetic variation.

Family-GWAS reveals effects of environment and mating on genetic associations

Family-based GWAS meta-analysis of 34 phenotypes shows standard GWAS effects carry sizeable confounding uncorrelated with direct genetic effects, while assortative mating likely inflates SNP heritability and genetic correlations.

Multi-ancestry polygenic risk scores for venous thromboembolism

This study develops multi-ancestry polygenic risk scores for venous thromboembolism using diverse GWAS data and shows improved predictive performance across European- and African-ancestry populations.

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

This paper introduces SBayesRC, a method that improves polygenic prediction of complex traits by integrating GWAS summary statistics with functional genomic annotations, showing significant accuracy gains across ancestries.

Larger cerebral cortex is genetically correlated with greater frontal area and dorsal thickness

The paper investigates the genetic architecture of cortical expansion and regionalization by comparing genome-wide association studies of 24 cortical regions with and without adjustment for global measures, finding distinct genetic loci associated with different regions.

OTTERS: A powerful TWAS framework leveraging summary-level reference data

OTTERS is a TWAS framework that uses summary-level eQTL reference data to estimate eQTL weights and perform omnibus TWAS, showing improved power and applicability.

Rare Genetic Variants Underlie Outlying levels of DNA Methylation and Gene-Expression

This study identifies rare genetic variants associated with extreme DNA methylation levels and shows their impact on gene expression in healthy ageing populations.

Phenotypic and genetic factors are associated with absence of cardiomyopathy symptoms in PLN c.40_42delAGA carriers

The paper identifies shorter QRS duration in asymptomatic PLN c.40_42delAGA carriers and links it to genetic sensitivity in symptomatic carriers.

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

mBAT-combo improves gene-trait association detection in GWAS by accounting for SNP effect directions, revealing masking effects in complex traits.

Local CpG density affects the trajectory of age-associated epigenetic changes

The paper shows that local CpG density influences age-related DNA methylation changes in humans by analyzing longitudinal methylation data and SNP data from 600 individuals.

Improving GWAS discovery and genomic prediction accuracy in Biobank data

This paper improves genomic prediction and GWAS discovery in biobank data using a Bayesian grouped mixture of regressions model, achieving higher accuracy and detecting more loci than existing methods.

Assortative Mating Biases Marker-based Heritability Estimators

The paper shows that marker-based heritability estimators are biased under assortative mating and proposes corrected estimators for traits under equilibrium assortative mating.

Epigenetic scores for the circulating proteome as tools for disease prediction

The paper develops epigenetic scores (EpiScores) for plasma proteins to predict disease risk, finding 137 associations with incident morbidities independent of known factors.

Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors

This paper introduces DENTIST, a method to reduce errors and heterogeneity in GWAS summary data, improving analyses like COJO and fine-mapping.

Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits

The paper introduces a Bayesian model, BayesRR-RC, to infer the genetic architecture of complex traits and finds that most genetic variance is attributed to non-proximal regulatory and coding regions.

Resource Profile and User Guide of the Polygenic Index Repository

The paper constructs polygenic indexes for 47 phenotypes across 11 datasets and provides a tool to correct errors-in-variables bias when using PGIs as proxies for the additive SNP factor.

Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals

This study estimates non-additive genetic variance in human complex traits using a large sample of unrelated individuals and finds that additive variance is predominant while dominance and epistatic variances are negligible.

Quantifying genetic heterogeneity between continental populations for human height and body mass index

The paper quantifies genetic heterogeneity between European and African populations for height and BMI, finding high shared genetic variation suggesting GWAS findings in Europeans are applicable to non-Europeans.