GWAS summary statistics

OmicsPred as a centralised resource for genetic prediction of multi-omic traits

OmicsPred collects 3,339,469 genetic prediction models for transcript, protein and metabolite traits with harmonised metadata and MetaXcan/PGSC-Calculator files, plus multi-ancestry Million Veterans Program phenome-wide association results.

POISE: Spectral Inference of Parent-of-Origin Effects in Unlabeled Genomic Data

POISE infers parent-of-origin effects in unlabeled genomic data using spectral decomposition and bootstrap confidence intervals, identifying 134 new variants in lipid metabolism and immune regulation from UK Biobank data.

Robust Inference of Individualized Treatment Effect in Mendelian Randomization

This paper develops a robust method for inferring individualized treatment effects in Mendelian randomization, showing improved coverage and shorter intervals compared to existing methods.

Multi-ancestry genome-wide association study and meta-analysis of stimulant use disorder reveals biology and relationships to other psychiatric disorders

This paper conducts a multi-ancestry GWAS of stimulant use disorder, identifies 19 genome-wide significant loci, and finds genetic correlations with other psychiatric and substance use disorders.

Separating direct, indirect and parent-of-origin genetic effects in the human population

The paper introduces JODIE, a model to estimate direct, indirect, and parent-of-origin genetic effects on height, BMI, and educational attainment using family trios from two biobanks.

Distinct and shared genetics of kidney filtration function versus albuminuria revealed by multi-trait GWAS

This study performs a multi-trait GWAS on kidney filtration function and albuminuria, identifying distinct genetic signals and shared mechanisms.

Partitioning Fraction of Variance Explained into Strong Localized Effects and Weak Diffuse Effects

The paper introduces a decomposed FVE estimation framework to improve heritability estimates by accounting for heavy-tailed SNP effects and violations of the bounded-kurtosis condition.

GLOF: A large-scale expert-curated benchmark dataset of gain-of-function and loss-of-function missense variants

The paper introduces GLOF, a large-scale expert-curated dataset of missense variants classified as loss-of-function, gain-of-function, or neutral, to benchmark computational methods for predicting variant functional mechanisms.

An Agentic Platform for Drug Repurposing Unified across Molecular, Phenotypic, and Clinical Scales

LinkD is a drug repurposing platform that integrates molecular, phenotypic, and clinical data to prioritize drugs, showing reduced prostate cancer incidence with beta-blockers.

Contextualizing the Utility of Polygenic Risk Scores using Absolute Risk Models in Diverse Ancestry Populations

This paper evaluates polygenic risk scores (PRSs) in diverse populations using absolute risk models, finding that PRSs can provide greater utility in risk stratification for certain diseases in non-European populations.

Modelling cognitive outcomes in the UK Biobank: education, noradrenaline and frontoparietal networks

The paper models how education interacts with neurobiological features to influence cognitive outcomes in the UK Biobank cohort, showing that right fronto-parietal connectivity mediates this effect.

Breast cancer polygenic risk score performance varies by socioeconomic status

This study shows that breast cancer polygenic risk scores perform differently across socioeconomic statuses, with income improving predictive accuracy in certain groups.

Trans-ancestry genome-wide association meta-analysis of antidepressant response to selective serotonin reuptake inhibitors in clinical studies of depression

This study performs a trans-ancestry GWAS of SSRI response in depression, finding suggestive associations and enrichment in serotonergic pathways but no genome-wide significant variants.

Ultra-Fast Implementation of Multivariate GWAS in Genomic SEM Using Flexible Analytic Estimation

The paper introduces an ultra-fast analytic solution for multivariate GWAS in Genomic SEM, reducing computation time by over 800 times and enabling efficient analysis on standard hardware.

Orchestrating multi-state QTL analysis with Bioconductor

The paper introduces two Bioconductor packages for multi-state QTL analysis, providing tools for data storage, analysis, and simulation.

Genomic Informational Field Theory (GIFT) to identify genetic associations of a complex trait using a small sample size

This paper introduces GIFT, a method that enables accurate genetic association analysis in small datasets, identifying loci linked to height at withers in ponies and validating a hypothesis about insulin physiology.

Leveraging the Genetics of Psychiatric Disorders to Prioritize Potential Drug Targets and Compounds

This paper uses genetic data from psychiatric disorders to prioritize drug targets and compounds, identifying genetic support for existing medications and opportunities for drug repurposing.

Circular RNA-associated QTLs show stronger association with splicing-QTLs than with expression-QTLs

The paper compares circQTLs with splicing and expression QTLs, finding stronger genomic overlap with splicing-QTLs and distinct genomic distribution patterns.

Positive-control Mendelian randomization highlights power constraints in disease-mortality GWAS

The paper uses Mendelian randomization to show that current disease-mortality GWAS may lack sufficient power to detect shared genetic effects, despite strong associations in case-control studies.

Estimation of Direct and Indirect Polygenic Effects and Gene-Environment Interactions using Polygenic Scores in Case-Parent Trio Studies

This paper introduces PGS-TRI, a framework to estimate direct and indirect polygenic effects and gene-environment interactions in case-parent trio studies, applied to autism and orofacial clefts.

Evaluation of epistasis detection methods for quantitative phenotypes

This study evaluates six epistasis detection methods for quantitative phenotypes using simulated data and the ABCD dataset, finding varying performance across interaction types.

A pilot genome-wide association and gene-level prioritization analysis of ischemic heart disease with co-occurring arterial hypertension in a Kazakh cohort

This paper conducts a GWAS of ischemic heart disease with arterial hypertension in a Kazakh cohort, finding no significant SNPs but prioritizing candidate genes using MAGMA and KGWAS methods.

Reproducibility of the evaluation of genetic variant pathogenicity based on the animal variant classification guidelines

This study assesses the reproducibility of pathogenicity classification using the animal variant classification guidelines across three species, finding 65% reproducibility for pathogenicity and 83% clinically relevant agreement.

Multi-ancestry, trans-generational GWAS meta-analysis of gestational diabetes and glycaemic traits during pregnancy reveals limited evidence of pregnancy-specific genetic effects

The paper conducts a multi-ancestry, trans-generational GWAS meta-analysis of gestational diabetes and glycemic traits, identifying novel loci and highlighting limited pregnancy-specific genetic effects.

A Comparative Survey of Functional Evidence Use in Hearing and Vision Loss Genetics

The paper surveys genetics professionals on their use of functional evidence in variant classification for hearing and vision loss, highlighting challenges in data quality, accessibility, and integration into clinical practice.

Locally adaptive conformal prediction intervals for polygenic score-based phenotype prediction via residual normalization and data-driven stratification

This paper introduces C-SCNR, a framework for constructing calibrated prediction intervals for polygenic score-based phenotype prediction, outperforming existing methods in diverse error distributions and subgroups.

An Expectation and Maximization Algorithm for Multivariate Genome-wide Association Studies (EMmvGWAS)

EMmvGWAS improves multivariate GWAS efficiency by using an EM algorithm to reduce computation time while maintaining statistical power.

A gene-distal polygenic architecture underlies the dominant axis of human trait covariation

This study identifies a gene-distal polygenic architecture underlying a dominant axis of human trait covariation, showing structured cross-trait information in the sub-significant polygenic background.

Conditional and marginal SNP-heritability to leverage ancestral and environmental diversity

The paper introduces a conditional SNP-heritability method to estimate heritability across subpopulations with different ancestral and environmental factors, showing how heritability of intelligence scores varies by socio-economic group.

PRISMA: A tensor-based framework for deconstructing the genetic architecture of complex diseases, with application to diabetic retinopathy

PRISMA decomposes GWAS signals into tissue-specific genetic axes for diabetic retinopathy, revealing novel targets and regulatory patterns.