GWAS / association mapping

This paper introduces Manc-COJO, a method for multi-ancestry conditional and joint analysis of GWAS summary statistics, improving detection of independent signals and reducing false positives.

The paper develops a statistically optimal test for gene-gene interaction that accounts for main effects, showing improved power over existing methods in simulations and identifying pathway-related SNP pairs in IBD data.

This study investigates the role of SORL1 genetic variants in AD, RD, and PD across diverse populations, identifying variants associated with risk but no significant cumulative effect.

The paper identifies tri-SNP haplotypes in HLA-DRA associated with type 1 diabetes and celiac disease, and links them to differences in complement system genes C4A and C4B.

The paper integrates chromatin accessibility data with GWAS to identify regulatory mechanisms underlying blood lipid traits, finding 20% of signals lack proposed mechanisms.

PETScan performs genome-wide association analysis of RNA-Seq and ATAC-Seq data using negative binomial models and score tests, achieving faster computation than Wald tests while identifying similar significant gene-peak pairs.

This paper identifies 58 genome-wide significant loci for major anxiety disorders using a large meta-analysis and highlights GABAergic signaling as a potential mechanism.

This study identifies loci and mutations associated with pyrethroid resistance in Anopheles gambiae species complex using multi-omics data and finds potential diagnostic markers and introgression between species.

This study develops M-cTWAS to integrate multi-omics and multi-context QTL data with GWAS, improving the discovery of risk genes for complex traits.

This study integrates metabolomic and genetic data from the CARDIA study to identify novel variants associated with metabolite levels across diverse populations.

The paper integrates multi-omic QTLs and predictive models to identify regulatory variants in CD4+ T cells and their role in immune-related GWAS loci.

This study uses pQTL-based Mendelian randomization and colocalization to assess if DMARD targets reduce Alzheimer's disease risk, finding only FCGR3B shows increased risk with higher plasma levels.

This study identifies shared genetic risk between major depression and atherosclerotic diseases and links causal gene expression changes in blood, brain, and heart tissues to depression etiology.

The paper identifies lymphatic reflux dysfunction as a driver of sepsis by showing that VEGFR3-SOX18-HSPG2-heparan sulfate disruption impairs lymphatic barrier function and promotes systemic inflammation.

This study examines sex and race differences in LDL-C levels and statin treatment using All of Us data, finding higher LDL-C in women and lower statin use and efficacy in women, especially Black women.

COLSTATS provides a web platform for colocalizing GWAS and QTL summary statistics to identify shared genetic determinants.

This study introduces PleioSDPR, a method that improves polygenic risk prediction by jointly modeling genetic effects across correlated traits, showing significant accuracy gains in real trait applications.

This paper develops a polygenic risk score for glaucoma with improved performance across major ancestries, enabling earlier detection and targeted treatment of high-risk individuals.

This study investigates ANO6's role in Parkinson's disease by analyzing common and rare variants across large datasets, finding no strong genetic association.

This study identifies genetic relationships between substance use disorders and externalizing/internalizing psychopathology, finding that internalizing contributes uniquely to SUD risk.

The paper conducts a GWAS in the Portuguese population to identify migraine risk loci, finding a novel association with the NPS gene and highlighting potential therapeutic targets.

This study identifies 68 genes associated with drought tolerance in Arabidopsis thaliana seedlings using GWAS and validates their roles through reverse genetics.

The paper uses a MAGIC population to study genetic architecture of clinal traits in Mexican maize, finding one major QTL for tassel branching and multiple QTL for flowering time with complex environmental associations.

The paper shows that phenotype scale choice affects GxE signals in biobank data, with log scaling revealing meaningful effects and explaining a significant portion of PGSxSex interactions.

The paper identifies 508 CKD-associated genetic loci, prioritizes 651 kidney genes, and highlights novel CKD genes like CA12 with functional consequences.

The paper identifies a causal link between chronic pain genetics and late-onset asthma through the nervous system using genome-wide association and Mendelian randomization analyses.

The paper identifies risk loci for acute respiratory distress syndrome (ARDS) by analyzing protein quantitative trait loci (pQTLs) from GWAS of sepsis-related biomarkers.

The paper develops a taxonomy-free GWAS method using k-mers to analyze gut microbiome associations with host phenotypes, identifying significant links to seven traits in a cohort of healthy participants.