GWAS / association mapping

Deep transcriptomic analysis of molecular mediators of complex traits in heterogeneous stock (HS) rats

This paper expands the RatGTEx resource with transcriptome-wide associations across 3,160 RNA-seq samples, identifying 7,473 gene-trait links and 144,876 QTLs for 22,599 genes.

Shared additive- and variance-associated genetic architecture of cardiac structure and function

The paper identifies shared and distinct genetic architectures for cardiac structure and function using UK Biobank data, revealing common variants influencing multiple chambers and phenotypic variability.

Evolution-guided association mapping using long-read genomes from a self-identified Black or African American cohort in All of Us

This study uses long-read genomes from a Black or African American cohort to identify genomic regions under recent positive selection and their associations with phenotypes.

High-throughput sequencing of unmethylated DNA (UMR-seq) reveals extensive epigenetic variation in the hypomethylome of diverse plant species

UMR-seq reveals epigenetic variation in plant hypomethylomes, showing UMRs are enriched in regulatory loci and improve genomic prediction and trait association mapping in wheat.

Novel Regulators of Sugar-dependent Food Consumption in Drosophila melanogaster

This study identifies genetic regulators of sugar-dependent food consumption in Drosophila using GWAS and RNAi knockdown.

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.

Quantifying heritability in functional regions of the coding and non-coding genome across diverse individuals

The paper estimates whole-genome heritability of complex traits across diverse populations, finding rare and non-coding variants significantly contribute to heritability.

The genetic architecture of human DNA methylome variation

This study develops pangenome-based frameworks to analyze DNA methylome variation across diverse human genomes, identifying genetic factors influencing methylation patterns and their associations with complex traits.

Genetic and Epigenetic Landscape of Self-Identified Hispanics/Latino in All Of Us

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

Integrating pangenome and imputation framework reveals structural variants affecting stature and milk composition traits in French dairy cattle

The paper integrates long-read, short-read, and SNP data using a pangenome and imputation framework to identify structural variants associated with stature and milk traits in dairy cattle.

Single-cell transcriptome-wide association analysis reveals epithelial cell-specific genetic susceptibility to colorectal cancer

The paper performs single-cell transcriptome-wide association analysis to identify cell-type-specific genetic susceptibility genes for colorectal cancer, finding 546 gene-cell-type associations and 347 candidate susceptibility genes.

Multimodal Analysis of Transcriptional Regulation in the Dorsolateral Prefrontal Cortex Enhances Alzheimer's Disease Risk Gene Discovery

This study uses multimodal transcriptomic data to enhance Alzheimer's disease risk gene discovery, identifying 161 risk genes with proteomic support and an interconnected network of hub genes.

Joint QTL mapping reveals patterns of pleiotropy across structured environments in budding yeast

The paper uses joint QTL mapping to analyze pleiotropy patterns across structured environments in budding yeast, revealing genetic interactions influenced by environmental relationships.

Genomic forecasting links climate-associated variation to spring phenology in the European wild apple, a crop wild relative of the cultivated apple

The paper tests if climate-associated genomic variation predicts phenotypic adaptation in European wild apple, finding genomic offsets link to bud-break timing but not other traits.

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.

Beyond single-trait analysis: ancient genomes reveal coordinated evolution of dietary endophenotypes in Holocene Europe

This study uses ancient genomes to show coordinated evolutionary changes in dietary endophenotypes across Holocene Europe.

A connection-level genetic atlas of human cortical functional connectivity at rest and during a task

The paper presents a connection-level genetic atlas of human cortical functional connectivity, identifying genetic loci associated with resting and task states.

SRSF1 coordinates transcription and alternative splicing to modulate p53 and apoptosis

This study identifies SRSF1's role in coordinating transcription and alternative splicing, showing its impact on p53 regulation and apoptosis across multiple cell lines and cancer cohorts.

Population genomics of Candida albicans reveals genetic footprints that allow the prediction of antifungal resistance

This study uses population genomics and machine learning to identify genetic markers predictive of antifungal resistance in Candida albicans, highlighting the need for expanded resistance catalogues.

Plasma Proteogenomics Identifies RGMB as a Candidate for Primary Open-Angle Glaucoma Detected Only in East Asians

The paper identifies RGMB as a potential risk factor for East Asian POAG through proteogenomic analysis, showing ancestry-specific associations and lack of colocalization with IOP traits.

Genomic signals of local adaptation in UK black alder populations (Alnus glutinosa)

The paper analyzes genomic data from UK black alder populations to identify loci associated with environmental adaptation and assesses maladaptation risks under climate change.

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.

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.

Tandem repeat variation shapes immune cell type-specific gene expression

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

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.

Identifying candidate genetic determinants associated with invasion in pneumococcal lineages

The paper identifies invasion-associated genetic variants in pneumococcal lineages by separating serotype and lineage effects, highlighting candidate determinants for experimental investigation.

Parkinson's disease genetic risk converges on Lewy body pathology-associated microglial states

The paper identifies microglial states associated with Parkinson's disease genetic risk and Lewy body pathology using single-cell profiling and integrates data with AMP PD.

LDscnR: LD-aware complexity reduction for genome scans

LDscnR reduces genome scan tests by grouping correlated markers using LD decay, improving precision while maintaining recall, and showing structure can explain outlier regions.

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.