GWAS summary statistics

LRCQ: phenome-wide heritability enrichment of genomic loci from GWAS summary statistics

LRCQ estimates phenome-wide heritability enrichment of genomic loci using GWAS summary statistics, identifying enriched regions and their functional annotations.

LRCP: identifying functionally related SNPs and genes from phenome-wide genetic-effect correlations using GWAS summary statistics

LRCP identifies functionally related SNPs and genes by estimating phenome-wide genetic-effect correlations from GWAS summary statistics, improving accuracy over naive methods.

Genome-wide meta-analysis of pilonidal sinus disease and its genetic overlap with hidradenitis suppurativa, hair patterning and adiposity

This study identifies genetic risk loci for pilonidal sinus disease and finds strong genetic overlap with hidradenitis suppurativa and hair patterning, but not obesity.

Polygenic evolution towards a morning chronotype in modern humans

This study identifies polygenic trends in morning chronotype evolution in modern humans above 20 degrees north, showing increased morningness compared to Neanderthals.

Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model

The paper benchmarks variant effect predictors using a leakage-controlled dataset and develops a gradient-boosting consensus model that outperforms existing tools.

Ancestry-specific and multi-ancestry genome-wide association studies of restless legs syndrome

This study conducts ancestry-specific and multi-ancestry GWAS of restless legs syndrome, identifying shared and ancestry-specific risk loci across African, Latin American, and European populations.

Long-range chromatin interactions nominate candidate susceptibility genes at non-coding PDAC risk loci

The paper fine-maps GWAS risk variants for PDAC and identifies candidate target genes through chromatin conformation capture, finding functional interactions and eQTLs at specific loci.

BLocPRS: locus-aware ensembles of polygenic scores provide accurate linear prediction

BLocPRS improves polygenic risk score prediction by combining locus-specific weights from different PRSs, achieving higher accuracy in UK Biobank and extending to non-European populations.

Genetics in Context: Social Factors Modify Polygenic Risk Across Multiple Cardiometabolic Diseases

The paper examines how social determinants of health modify polygenic risk scores for cardiometabolic diseases and shows that integrating social and genetic factors improves disease prediction.

Gene-by-Sleep Duration Interaction for Glycemic Traits in over 480,000 Individuals

The paper identifies 16 genetic loci interacting with sleep duration to influence glycemic traits in over 480,000 individuals, revealing distinct biological mechanisms for short and long sleep.

MutQA: A Cross-Validated Q&A Dataset for Genetic Mutations

The paper introduces MutQA, a cross-validated Q&A dataset linking genetic mutations to their functional consequences, and demonstrates its utility in improving LLM performance.

Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression

Single-cell eQTL mapping in 5.4 million PBMCs from 1,925 individuals with matched WGS finds common-variant eQTLs for 83% and rare-variant signals for 47% of 21,404 genes.

Network Analysis of Rare Single-Nucleotide Polymorphisms Suggests a Central Role for Type 17 Immune Responses in Trauma-induced, Genotypically Associated Hypo-Inflammation and Critical Illness

The paper identifies rare SNPs associated with hypo-inflammation and adverse outcomes in trauma patients, highlighting type 17 immune responses as central to critical illness.

Genetic axes of hand and shoulder soft-tissue disease and their divergent responses to adiposity and incretin therapy: a cross-biobank genomic and randomised trial study

This study identifies two genetically distinct axes of hand and shoulder soft-tissue disorders and shows divergent responses to adiposity and incretin therapy.

Fast Probabilistic Whitening Transformation for Ultra-High Dimensional Genetic Data

The paper introduces a probabilistic whitening transformation for high-dimensional genetic data, showing it is faster and more accurate than existing methods for imputing z-statistics and identifying genetic regulatory signals.

Scaling genetic discovery through automated post-GWAS interpretation

This paper introduces PGI, a system that automates post-GWAS interpretation, achieving high recovery of findings and enabling cross-study biological evidence accumulation.

Comprehensive adjudication identifies 111 high-confidence loci for Alzheimer's disease and related dementias

The paper systematically adjudicates genetic evidence for Alzheimer's disease and related dementias, identifying 111 high-confidence loci through a tiered framework applied to large-scale genome-wide studies.

Variant effect predictors are shaping the ClinVar classifications used to train and evaluate them

The paper shows that variant effect predictors influence ClinVar classifications, creating circularity in variant classification and prediction.

A family-aware All of Us benchmark for polygenic prediction and genomic machine learning

The paper introduces a family-aware benchmark for polygenic prediction using All of Us data, enabling comparison of PRS and machine learning models across 14 traits with strong predictive performance.

Genetic Modifiers of Age at Onset for Parkinson's Disease in European Populations

This study identifies five genetic loci associated with age at onset of Parkinson's disease in European populations, including novel associations at HIP1R and FSCB.

A Polygenic Score for Smoking Persistence Captures Differences in Cessation Age

This paper develops a polygenic score for smoking persistence and finds it is associated with earlier or later cessation ages across diverse populations.

A Pipeline for Predicting Variant Associations with Complex Disorders via Functional Annotations

The paper introduces a pipeline to create curated, balanced variant-trait association datasets for complex disorders using GWAS and functional annotations.

Haplotype-based fine-mapping of variant associations for complex traits

This paper introduces a haplotype-based fine-mapping method called happler to identify causal variants for complex traits, showing improved performance over traditional methods in detecting haplotype effects.

GWAS of Lyme disease identifies five loci and discovers a connection with post-infectious diseases

This study conducts a GWAS of Lyme disease, identifying five genetic loci and linking it to post-infectious diseases like Bell palsy and joint pain.

Insomnia and the genetic overlap of sleep with depression and anxiety: a genomic structural equation modelling study

This study uses genomic structural equation modelling to assess the genetic overlap between insomnia, depression, and anxiety, finding insomnia is the best-supported location of the genetic overlap.

Genome-wide LD scores enable robust heritability and genetic correlation estimation from summary statistics across genetic ancestries

SUMMIT improves heritability and genetic correlation estimation across diverse ancestries using LD scores and GWAS summary statistics, showing better accuracy in non-European populations.

Population-scale drug target and variant prioritization with Varformer

Varformer prioritizes drug targets and variants by integrating variant and gene features using a transformer model, achieving high precision across diverse benchmarks.

LKOM: Longitudinal Knockoff with Masked Likelihood Ratio for FDR-Controlled Association Discovery

LKOM identifies genetic variants associated with longitudinal phenotypes by jointly modeling mean and variability signals while controlling the false discovery rate.

S4-Oligo: optimizing polygenic score methods for clinical deployment

This paper introduces S4-Oligo, an optimized polygenic score method for clinical use, which matches or exceeds existing models' accuracy while using fewer SNPs.

Multivariate genetic analysis maps shared biology between psoriasis and cardiovascular diseases