GWAS / association mapping

PANACEA improves GWAS meta-analysis by using a continuous ancestry representation to include more diverse participants and increase statistical power.

This study compares genomic signatures of natural selection across Senegalese, Thai, and Peruvian populations to identify immune-related adaptive variants with implications for region-specific vaccine development.

This study performs multi-environment GWAS on photosynthetic light use efficiency in Arabidopsis thaliana, identifying robust and conditional quantitative trait loci.

The paper identifies genetic factors and pathways associated with putamen volume using GWAS data from the ABCD study and finds shared genetic architecture with neuropsychiatric disorders.

The paper investigates genetic variants and oral contraceptive use interactions on depression risk in the UK Biobank, finding no genome-wide significant interactions.

This study identifies genetic loci associated with grain iron and zinc concentrations in wheat under different moisture conditions using genome-wide association analysis.

Contrasting a pretrained genomic language model's attention between case and control haplotypes ranked HBB first on chromosome 11 and recovered more known β-thalassemia variants than GWAS, without per-variant tests.

The paper investigates the genetic role of SLC25A46 in Parkinson's disease, REM sleep behavior disorder, and Dementia with Lewy Bodies, finding no significant associations.

TLS-Tractor integrates external GWAS summary statistics with individual-level data for ancestry-aware association analysis in admixed populations, improving power and calibration.

This study shows that common GWAS methods can produce misleading associations in livestock with polygenic architecture, highlighting the need for methods that control long-range LD spillover.

The paper characterizes common human polymorphic inversions and their functional effects, showing they are enriched in functional variants and associated with phenotypic traits.

In 14 BXD mouse strains, those modelling developmental coordination disorder have relatively larger cortex and smaller cerebellar/subcortical volumes; this axis tracks motor coordination but maps to no single QTL.

FORGEPHAST simulates large synthetic cohorts with controlled genetic and phenotypic properties, showing polygenic risk score performance varies by phenotype architecture, ancestry, and variant coverage.

The paper introduces EdgeMap to assess conditional heritability of ligand-receptor gene annotations in spatial transcriptomics data, finding higher edge z-scores in biologically matched tissues.

This study uses Mendelian randomization and mediation analysis to show that neuroticism's link to Alzheimer's disease is mediated by modifiable factors like depression, hypertension, and alcohol consumption, rather than being causal.

This paper identifies a proteomic and metabolomic pathway linking insulin resistance to coronary heart disease through genetic analysis and mediation modeling.

GraNPA identifies phenotype-associated genomic regions using pangenome graphs with few individuals, achieving GWAS-like results without population materials or kinship data.

The paper analyzes the impact of CYP2C19 genotype on SSRI side effects and discontinuation rates in a large sample of individuals.

This paper introduces SimPhyNI, a framework for microbial GWAS that improves precision and recall in detecting gene-gene and gene-trait associations in bacterial genomes.

The paper identifies a conserved metabolic and genetic architecture linked to cognitive plasticity and psychiatric conditions, showing that extreme cognitive abilities and schizophrenia share a common genomic basis governed by metabolic constraints.

This study evaluates the technical and biological reliability of 18 epigenetic clocks and shows that technical reliability does not predict biological reliability, which is critical for clinical applications.

This study identifies time-dependent epistatic interactions between Oprm1 and Fgf12 that modulate opioid-induced locomotion in mice and links Fgf12 to opioid behavior in humans.

This study identifies genetic risk loci for doxorubicin-induced arrhythmia through GWAS meta-analysis and validates their functional relevance in human and zebrafish models.

This study identifies 26 risk loci for fibromyalgia through a genome-wide association analysis of 2.5 million individuals, revealing genetic links to neural functions and chronic pain disorders.

This paper introduces a method to prioritize non-coding variants in rice GWAS loci using a chromatin-informed DNA language model, demonstrating its utility through case studies.

This study identifies genetic loci associated with fibromyalgia and finds strong genetic correlations with psychiatric and medical traits.

This study investigates genetic overlaps between psychiatric disorders, cardiometabolic diseases, and brain structure to understand shared and distinct genetic pathways contributing to comorbidity.

This study expands the human plasma proteome analysis using an enhanced SomaScan platform, identifying new genetic associations and disease mechanisms beyond the classical secretome.