GWAS summary statistics

Genome-wide association study in a diverse grapevine collection provides insights into the genetic basis of berry size and cluster architecture traits

This study performs a GWAS on a diverse grapevine collection to identify genetic determinants of berry size and cluster architecture traits, finding significant SNPs and candidate genes.

Genome-wide cross-trait analysis of vascular dementia and Alzheimer's disease highlights novel loci and lung-brain axis

This study identifies novel genetic loci for vascular dementia and its association with lung function, and finds shared genetic risk factors with Alzheimer's disease.

Language models reveal evidence gaps in variants of uncertain significance

The paper uses language models to analyze ClinVar variant summaries, identifying evidence gaps in Variants of Uncertain Significance and reclassifying some as likely benign or pathogenic.

MetaOmixTools: an interactive web suite for meta-analysis of ranked features and functional enrichment

MetaOmixTools provides a web-based platform for meta-analysis of ranked features and functional enrichment, enabling integration of multi-study omics data to identify conserved biological insights.

NetCrafter: Ontology-derived gene network modeling and interpretation

NetCrafter constructs context-specific gene networks using ontology-weighted similarity, enabling functional interpretation and identification of interaction hotspots.

Genetic correlation analysis identifies TMEM106B, ACE, and ERC2 as genetic loci shared between Alzheimer's disease and primary psychiatric disorders

Computation and resource efficient genome-wide association analysis for large-scale imaging studies

This paper introduces RVGA, a framework for efficient genome-wide association analysis in imaging genetics, identifying novel loci and genetic correlations in brain structures using UK Biobank data.

PHARMWATCH: A Multilayer Pharmacogenomics Safety System for Accurate Star Allele Interpretation

PHARMWATCH improves pharmacogenomics safety by identifying genomic alterations that affect star allele accuracy, enabling more reliable drug dosage recommendations.

Statistical uncertainty explains the poor agreement in polygenic scoring for type 2 diabetes

The paper shows that statistical uncertainty explains disagreement in type 2 diabetes polygenic scores and proposes using uncertainty measures to improve risk prediction.

Inferring genotype-phenotype maps using attention models

This paper applies attention-based models to predict phenotype from genotype, showing improved performance in epistatic regimes and enabling transfer learning across environments.

Evidence for sexual antagonism and antagonistic pleiotropy in the maintenance of late onset Alzheimer's disease alleles

The paper investigates the role of sexual antagonism and antagonistic pleiotropy in maintaining late-onset Alzheimer's disease alleles, finding evidence of sexually dimorphic genetic effects and an inverse relationship with cancer risk.

Genetic Evidence for Opposing Associations of Psoriasis and Type 2 Diabetes with Inflammatory Bowel Disease: A Mendelian Randomization Study

This study uses Mendelian randomization to explore causal relationships between psoriasis, type 2 diabetes, and inflammatory bowel disease, finding positive associations for psoriasis and inverse for type 2 diabetes with ulcerative colitis.

Shared genetic factors between lung function and asthma by age at onset

This study identifies shared genetic factors between asthma and lung function that vary by age-at-onset, highlighting distinct mechanisms for early-onset asthma.

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.

Testing for gene-environment (GxE) interaction using p-value aggregation identifies many GxE loci

This paper introduces a p-value aggregation method to detect gene-environment interactions, identifying more loci than traditional additive models in UK Biobank data.

Genome-wide association study of extrapulmonary traits in the context of COPD

This study identifies genetic variants associated with extrapulmonary traits in COPD using genome-wide association analysis across two cohorts.

Performance of a Type 1 Diabetes Genetic Risk Score in a Multi-centric Study from India and its Implications in Clinical Practice

This study evaluates the performance of a type 1 diabetes genetic risk score in Indian populations, finding it effective for classification but with variations based on autoantibody status and age at onset.

A time-to-event heritability framework for inferring the genetic architecture of longitudinal traits

This paper introduces COXMM, a model for estimating heritability of time-to-event traits, showing it outperforms non-TTE methods and reveals heritability patterns in longitudinal data.

Shared Genetic Liability across Systems of Psychiatric and Physical Illness

This study uses genomic structural equation modeling to identify genetic overlaps between psychiatric and physical illnesses, finding shared risk factors across multiple domains.

Building The Human Genotype-Phenotype Map to Harness Pleiotropy and Refine Disease Mechanisms

The paper introduces GPMap, a resource that maps genetic associations across traits and molecular measurements to identify pleiotropy and improve disease mechanism understanding.

Performance Characteristics of Reasoning Large Language Models for Evidence Extraction from Clinical Genomics Literature

This paper evaluates large language models for automated PS4 evidence extraction from clinical genomics literature, finding high accuracy but model-dependent performance.

Self-reported health history from 70,724 individuals reveals novel HLA associations with allergy and other frequently underreported conditions

This study identifies 15 novel HLA associations with underreported conditions using high-resolution HLA genotypes and self-reported health data from 70,724 individuals.

Short tandem repeats significantly contribute to the genetic architecture of metabolic and sensory age-related hearing loss phenotypes

The paper investigates the contribution of short tandem repeats (STRs) to age-related hearing loss phenotypes, finding they explain some missing heritability and identify risk associations.

Genetic underpinnings of chills from art and music

This study identifies genetic factors influencing susceptibility to chills from art and music using large-scale genetic data from 15,606 individuals.

GLP1R expression protects against 58 diseases but raises risk for 34 diseases and neonatal health

The paper uses Mendelian Randomization to evaluate GLP1R expression and CETP concentration on 396 diseases, finding 58 protective and 34 risk effects for GLP1R, with notable risks for neonatal health and age-related diseases.

Simplifying Systems Genetics with QTLretrievR: An R Package for Molecular QTL Identification

QTLretrievR simplifies molecular QTL identification in genetically diverse populations by integrating existing tools with parallelization, reducing computational time and improving accessibility.

Three Sibling Genes Involved in Genetic Risk for Lateral Epicondylopathy

This study identifies two genome-wide significant loci associated with lateral epicondylopathy, implicating SIBLING genes in extracellular matrix remodelling and challenging prior collagen gene associations.

Genome-wide Association Study of Social Isolation in 63 497 Japanese Individuals from the General Population

This study identifies genetic loci associated with social isolation in a Japanese population using GWAS, finding associations with ACADSB, HMX3, LINC02315, and LRFN5.

SMECT: a framework for benchmarking post-GWAS methods for spatial mapping of cells associated with human complex traits

SMECT benchmarks post-GWAS methods for spatial mapping of cells associated with human complex traits, revealing trade-offs between sensitivity and specificity across methods.

Impact of control selection strategies on GWAS results: a study of prostate cancer in the UK Biobank

This study evaluates control selection strategies in prostate cancer GWAS using UK Biobank data, finding that matched controls balance power and cost but may miss novel associations.