GWAS summary statistics

Multivariate genetic analysis maps shared biology between psoriasis and cardiovascular diseases

Polygenic prediction of treatment response for precision medicine is vulnerable to collider bias

This paper shows that polygenic risk scores for CAD can create false treatment response patterns due to collider bias, not actual biological effects.

Disentangling phenotype scale, amplification, and effect heterogeneity underlying polygenic GxE architecture of complex traits

This paper introduces REGENA, a method to disentangle gene-environment interaction mechanisms, finding that half of significant GxE signals are scale-dependent and effect heterogeneity drives most remaining GxE heritability.

Large language model classifies prior evidence in gene-phenotype associations

PESTO classifies gene-phenotype associations as Novel, Hypothesized, Existing, or Established using a large language model and structured genetic evidence, identifying 7% as Novel and 21% as Hypothesized in 940 associations.

Accounting for gene action improves the accuracy of polygenic scores for some complex traits

This study introduces PGSa,d, a polygenic scoring framework that incorporates both additive and dominance effects, showing improved accuracy for traits with significant dominance contributions.

The stuff that dreams are made of: Genomics and biology of nightmares

This study identifies genetic risk loci for nightmare frequency and explores its genetic correlations with psychiatric traits.

Identification of pleiotropic genes and biological mechanisms underlying the shared genetic component between asthma, neuropsychiatric disorders, and substance use behaviors

The paper identifies pleiotropic genes and mechanisms linking asthma, neuropsychiatric disorders, and substance use behaviors through multi-trait GWAS and single-cell transcriptomics.

Genomic foundation models do not yet boost common variant discovery beyond standard functional annotations

This study evaluates genomic foundation models' ability to improve common variant discovery in GWAS and finds they do not outperform standard functional annotations.

A test for linkage disequilibrium in structured populations

The paper introduces a hypothesis test to detect linkage disequilibrium adjusted for population structure in human datasets.

Sequence-based variant-effect predictions reveal trait-specific regulatory-layer profiles of complex-trait heritability

The paper uses sequence-based variant-effect predictions to show that different regulatory layers contribute variably to the heritability of complex traits within tissues.

Understanding genetic and environmental complexity in phenotypic resemblance across relatedness in population-scale data

The paper evaluates non-linearities in phenotypic similarity versus genetic relatedness by analyzing three processes: imperfect tagging, assortative mating, and shared environments, using UK Biobank and All of Us data.

Sample overlap in genome-wide association meta-analysis: practical comparisons across significance thresholds

The paper evaluates the impact of sample overlap in GWAS meta-analysis across different significance thresholds and shows minimal impact when overlap is small.

The Multi-scale Copula Index (MCI): a new information-theoretic measure of association and its applications in functional cancer genomics

The paper introduces the Multi-scale Copula Index (MCI), an information-theoretic measure of association, and demonstrates its utility in cancer genomics for capturing contextual associations in complex datasets.

An integrated data exploration engine of knowledge, expression and genetic association for human transposable elements

TE-Dee integrates TE knowledge, expression, and genetic associations to provide a structured resource for TE biology and AI model training.

Melanoma germline genetics: immune, cancer driver, and Wnt signaling genes

This paper identifies 116 risk loci for melanoma through GWAS, links susceptibility to immunity and Wnt signaling, and develops a PRS improving risk prediction.

A Genome-Wide Association Study in the Chilean admixed population reveals four new loci for COVID-19 severity and susceptibility

The paper conducts a genome-wide association study in a Chilean admixed population to identify genetic loci associated with COVID-19 severity and susceptibility, finding four new loci.

CaPri: Bayesian Mendelian randomization for joint estimation of causal and pleiotropic effects

CaPri is a Bayesian Mendelian randomization framework that jointly estimates causal and pleiotropic effects, showing robust performance across varying pleiotropy proportions and real data applications.

Dog-human gene network colocalization links synaptic signalling and ubiquitination to compulsive disorders

This paper uses GWAS in dogs and humans to identify a gene network linked to compulsive disorders, revealing biological pathways not detectable in human studies alone.

Quantifying the genetic separability of disease subtypes

This paper introduces GenSep, a framework to quantify genetic separability of disease subtypes, showing current PRSs fall short of theoretical limits.

Spatiotemporal AI modeling of gene regulation and variant effects in the developing human brain

This paper introduces Seal, an AI framework that models gene regulation and variant effects in the developing human brain across multiple regions, cell types, and stages, identifying regulatory mechanisms linked to neuropsychiatric diseases.

Gene-environment interaction loci with signatures of mid- to late Holocene selection show evidence for diet-dependent genetic effects

The paper identifies gene-environment interaction loci showing signs of selection and diet-dependent genetic effects across human populations.

Genetic and Biological Pathways Underlying the Relations between Executive Functioning and Externalizing Behaviors

The paper identifies genetic and biological pathways linking executive functioning and externalizing behaviors using genome-wide association study data.

Decomposing polygenic risk of coronary artery disease into distinct biological processes

The paper decomposes polygenic risk of coronary artery disease into distinct biological processes using latent factor decomposition of genetic variants.

The landscape of polygenic score prediction accuracy and transportability across the phenome in ancestrally diverse populations

This study evaluates polygenic score prediction accuracy and cross-ancestry portability across 3,994 PGSs in diverse populations, identifying factors affecting their performance and equity.

Mapping polygenic risk scores to brain cells: insights for neurodegenerative diseases

The paper uses polygenic risk scores to analyze genetic contributions to neurodegenerative diseases across brain cell types, finding shared and disease-specific genetic risks.

Expression predictions inform molecular interpretation of Alzheimer's disease risk loci

The paper evaluates how expression predictions from sequence models correlate with genetic associations in Alzheimer's disease risk loci, finding modest but significant relationships that suggest their utility as complementary evidence.

Matrix-Mechanical Genetic Susceptibility and Reduced Inflammatory and Immediate-Early Programs in Keratoconus

This study identifies genetic susceptibility in keratoconus linked to extracellular matrix mechanisms and shows reduced inflammatory and immediate-early gene expression in corneal tissue.

Sex-aware Cross-tissue Regulatory Transformer Identified Sexually Dimorphic Alzheimer's Disease Risk Loci and Causal Cellular Circuit

The paper identifies sex-specific Alzheimer's disease risk loci using a sex-conditioned Transformer model and links them to cellular mechanisms and disease phenotypes.

Fine-mapping HLA-II haplotypes in Alzheimer's disease and healthy longevity reveals distinct associations with microglial HLA-II load and neuropathology

drugMR: A multi-omics pipeline for genetically anchored drug-target discovery

drugMR uses multi-omics data to identify potential drug targets and adverse effects by integrating GWAS and pQTL statistics with various statistical methods.