GWAS summary statistics

Current challenges in GWAS integration and fine-mapping for variant interpretation

This paper identifies challenges in GWAS integration and fine-mapping for variant interpretation and suggests a multi-modal approach for prioritizing causal variants.

Integrating multi-ancestry common and rare variant mapping accelerates therapeutic target discovery

This study integrates common and rare variant mapping across diverse populations to identify novel therapeutic targets, finding NRG4 as a candidate for preserving kidney function.

TrustPGS: When can a polygenic score be trusted? A per-individual reliability framework across ancestries

TrustPGS evaluates per-individual reliability of polygenic scores across ancestries by analyzing distributional patterns in diverse populations.

Recalibrating Mendelian randomization under winner's curse, sample structure and polygenicity

This paper introduces a multivariable Rao-Blackwellization method to correct Mendelian randomization biases from winner's curse, polygenicity, and sample structure, improving type-I error control and inference robustness.

Why linkage disequilibrium measures disagree: Fisher geometry of rare common haplotype structure

The paper analyzes why LD measures disagree in the rare-common regime by examining the geometric structure of the haplotype simplex under the Fisher information metric.

Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers

This paper surveys early-career researchers on their understanding and implementation of ethical guidelines for population descriptors in genomics, highlighting misconceptions and structural barriers.

Integration of genetic evidence to identify approved drug targets

The paper integrates genetic signals to improve drug target identification by comparing prioritization strategies across traits and showing that combining related disease data enhances performance.

Genetic dose-response modelling predicts drug mechanisms, dosing, and adverse events

VIDRA models genetic dose-response relationships to predict drug mechanisms, therapeutic potential, and adverse events using phenotypically associated variants.

Characterization of Leukodystrophy Penetrance Using Large-Scale Integration of Genomic Population Screening and Electronic Health Records

The paper integrates genomic screening with EHR data to assess leukodystrophy penetrance and phenotypic variability, finding reduced penetrance and broad phenotypic spectra in some cases.

Detecting domain-level organization in genome-wide association study summary statistics using frequency-impact-reliability profiles

This paper introduces FIR-GWAS, a framework that reveals domain-level organization in GWAS summary statistics by analyzing frequency-impact-reliability profiles across multiple traits and species.

Toward Clinical Implementation of Polygenic Scores for Substance Use Disorders: A Multi-Ancestry Study

The paper develops and validates polygenic scores for substance use disorders across multiple ancestries, finding clinically relevant performance in European and Latinx populations but not in African populations.

Genetic Determinants of Pulmonary Artery Size in over 50,000 Subjects with and without COPD

This study identifies 44 genetic loci associated with pulmonary artery diameter across COPD and population-based cohorts, highlighting shared causal variation between pulmonary and systemic vascular biology.

Atypical energy-related symptoms define biologically distinct subtypes of major depressive disorder

The paper identifies biologically distinct subtypes of MDD based on energy-related symptoms and finds genetic and metabolic differences between them.

Long-range regulatory target prediction reveals shared genetic background across ulcerative colitis, Crohn's disease, primary sclerosing cholangitis and ankylosing spondylitis

The paper uses targPred to predict gene targets of regulatory variants in four immune-mediated diseases, identifying shared and disease-specific genetic mechanisms.

Identification and Functional Characterization of Regulatory Variants in DPP9 Associated with COVID-19 Severity

The paper identifies and functionally characterizes regulatory variants in DPP9 associated with severe COVID-19 by analyzing genetic risk factors and their impact on gene expression and immune cell function.

State-Dependent Transcriptomic Collapse of the Brain's Lactate and Ketone Thermodynamic Sensors in Schizophrenia

The paper identifies structural genomic variances in the HCAR2/HCAR1 locus that disrupt thermodynamic sensing in schizophrenia, linking metabolic dysfunction to clinical symptoms.

Improved heritability partitioning and enrichment analyses using summary statistics with graphREML

This paper introduces graphREML, a likelihood-based method for heritability partitioning and enrichment analysis using GWAS summary statistics, showing greater power than S-LDSC.

ADAMIXTURE: Adaptive First-Order Optimization for Biobank-Scale Genetic Clustering

ADAMIXTURE improves genetic clustering for large datasets by combining EM with Adam optimization, achieving faster runtime and scalability without sacrificing accuracy.

Bridging Ancestry Gaps in Genomic Risk Prediction with Tabular Foundation Models

This paper improves genomic risk prediction across ancestry groups using instruction-tuned tabular foundation models, showing better performance in under-sampled populations.

An AI-Assisted Comparative GWAS Pipeline Identifies Candidate Sex-Biased Schizophrenia Loci near CYP26B1 and EXOC6B

The paper introduces an AI-assisted GWAS pipeline to compare genetic associations across psychiatric datasets, identifying sex-biased schizophrenia loci near CYP26B1 and EXOC6B.

Formation, persistence, and breakdown of carrier-set topology in linkage disequilibrium: empirical structure in 1000 Genomes and a two locus Wright Fisher model

The paper analyzes carrier-set topology in linkage disequilibrium using empirical data and a Wright-Fisher model, showing that topology and visibility are separable and that |D'| better distinguishes nested configurations than r2.

Integrating Genetic, Environmental, Cognitive, and Temperament Data for ADHD Prediction in Explainable Deep Learning Models

This study develops an explainable deep learning model to predict ADHD using genetic, environmental, cognitive, and temperament data, finding that temperament features significantly improve classification performance.

Genetic drivers of etiologic heterogeneity in thyroid cancer

This study identifies 51 genetic loci associated with thyroid cancer through a multi-ancestry GWAS and explores pleiotropic relationships to uncover mechanistic clusters and genetic subtypes.

Evaluating Polygenic Score Transferability for Lipid Traits in Underrepresented Populations: Evidence from Samoan Cohorts

The paper evaluates polygenic score transferability for lipid traits in Samoan populations using genome-wide imputed genotypes and finds meaningful performance for LDL-C with a genome-wide PRS-CS score.

scEPS integrates genetic and single-cell disease atlas data to provide granular mechanistic insights into complex human diseases

scEPS integrates GWAS and single-cell data to identify disease-associated cell neighborhoods by testing gene expression variance explained in disease contexts.

Genetically informed single-cell and spatial mapping of metabolic programs in human health and disease

The paper introduces gmMAP, a framework that integrates metabolite GWAS with single-cell and spatial transcriptomes to map metabolic programs at cellular and spatial resolution, revealing associations between exogenous metabolites and cellular states.

Decoding the regulatory genetic architecture of endometriosis using AlphaGenome

This paper uses AlphaGenome to prioritize endometriosis-associated variants with strong uterus-specific regulatory effects, identifying new candidate genes and refining GWAS loci.

Multiple instance fine-mapping: predicting causal regulatory variants with a deep sequence model

The paper introduces MIFM, a deep learning method to predict causal regulatory variants from GWAS data using weak labels and DNA sequences, improving cross-ancestry risk prediction and variant disentanglement.

Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort

This paper performs a large-scale GWAS meta-analysis of neuropathologic lesions in Alzheimer's disease and related dementias, identifying both known and novel genetic associations.

Genome-wide genetic overlap between fear-based disorders and generalised anxiety disorder

This study identifies genetic differences between fear-based anxiety disorders and generalised anxiety disorder using GWAS, finding partial genetic distinction and shared liability to internalising psychopathology.