fine-mapping

FM-GPT: Bayesian fine mapping for phenome-wide transcriptome-wide association studies

FM-GPT is a Bayesian fine mapping method that identifies causal genes in phenome-wide transcriptome-wide association studies, improving accuracy and reducing false positives.

Genetic dissection of a Solanum elaeagnifolium tertiary genepool introgression associated with 4-O-caffeoylquinic acid accumulation in eggplant

This study identifies a 4-O-caffeoylquinic acid (4-CQA) accumulation trait from S. elaeagnifolium introgressions in eggplant through fine mapping and metabolite analysis.

Pleiotropic genetic architecture linking schizophrenia and substance use disorders

This study identifies shared genetic architecture between schizophrenia and substance use disorders using GWAS and genomic methods, finding significant genetic correlations and bidirectional causal relationships.

Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data

This study infers the demographic history of Chinese and Indian rhesus macaque populations using PacBio HiFi long-read sequencing data, revealing a split time and population size changes.

Genetic and epigenetic convergence at MOBP links ALS and PSP

The paper identifies shared genetic and epigenetic mechanisms at the MOBP locus linking ALS and PSP, with distinct patterns from MSA.

Genomic Architecture of Migraine: A Multi ancestry GWAS Meta analysis of 2.5 Million Participants

This study conducts a multi-ancestry GWAS meta-analysis of 2.5 million participants to identify genetic variants associated with migraine and link them to biological pathways and therapeutic targets.

Conditional polygenic enrichment distinguishes causal from tagging disease-critical cell populations in single-cell RNA-seq

This paper introduces scDRS-FM, a method to distinguish causal from tagging disease associations in scRNA-seq data, showing it improves power and accuracy in identifying disease-relevant cell populations.

Benchmarking Bayesian colocalization methods in validating Mendelian randomization-identified targets

This study benchmarks four Bayesian colocalization methods to validate MR-identified protein-trait associations for cardiometabolic traits, finding SharePro most frequently supports significant associations.

Long-read sequencing reveals hidden structural complexity within Alzheimers disease-associated GWAS loci

The paper uses long-read sequencing to uncover structural complexity in Alzheimer's disease GWAS loci, showing that lead SNPs often miss key regulatory variants.

Inferring causal cell types of human diseases and risk variants from candidate regulatory elements

This paper introduces CT-FM and CT-FM-SNP methods to identify causal cell types and variants for diseases, finding most SNPs affect traits via a single cell type set.

TRIDENT: a framework for robust multi-trait GWAS identifies 66 novel multi-trait osteoarthritis signals

TRIDENT is a framework for robust multi-trait GWAS that identifies 66 novel osteoarthritis signals by combining earlier and larger GWAS meta-analyses and applying translational annotation.

SuSiNE: Genetic fine-mapping with signed functional priors and multi-basin ensembling

SuSiNE improves genetic fine-mapping by incorporating signed functional priors and multi-basin ensembling to better resolve LD ambiguity and uncertainty.

ATLAS: Population-Level Disease Locus Discovery via Differential Attention in Genomic Language Models

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 genetic basis of resistance to pathogens in rainbow trout: a meta-QTL analysis

This paper performs a meta-QTL analysis to identify genetic regions associated with pathogen resistance in rainbow trout, refining QTLs and identifying candidate genes involved in immune pathways.

Dissecting the Genetic Link Between Insulin Resistance and Coronary Heart Disease: A Multi-Trait GWAS and Proteomic-Metabolomic Mediation Analysis

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

Common schizophrenia heritability concentrates in an evolutionarily young, brain-regulatory subset of fine-mapped credible-set variants

The paper identifies a young, brain-regulatory subset of schizophrenia risk variants that concentrate heritability after accounting for age, frequency, and selection signals.

Controls-Only Quality Control Metric from Early GWAS Can Attenuate Gene-Sex Interaction Signals in Contemporary Large-Scale Studies

The paper introduces SPADE, a QC metric that reduces bias from gene-sex interaction signals in large-scale GWAS by adjusting for sex-specific disease prevalence and preserving informative variants.

Phenotyping replication is a major determinant of genomic predictive ability in sweet sorghum (Sorghum bicolor Moench)

The paper evaluates how phenotyping replication, training population size, and genomic relatedness affect genomic predictive ability in sweet sorghum breeding programs.

Leveraging the genetics of human face shape boosts the discovery of orofacial cleft risk loci

This study uses a pleiotropy-informed GWAS method to identify new orofacial cleft risk loci by leveraging genetic associations with facial shape.

The genetic architecture of milk urea concentration in dairy cattle differs across the lactation cycle

This study identifies lactation-stage specific QTL for milk urea concentration in dairy cattle breeds, highlighting pleiotropic effects and candidate genes.

Extending Genome-Wide Association Studies to admixed cohorts with high degrees of relatedness

The paper introduces Tractor-Mix, a mixed model method for GWAS in admixed cohorts with high relatedness, improving ancestry-specific association detection and controlling false positives.

PanvaR: An R package for fine-mapping and visualizing results from genome-wide association studies

PanvaR integrates GWAS and fine-mapping in one tool, providing LD analysis, SNP effect predictions, and candidate gene lists with visualizations.

CuGen: A GPU-accelerated framework for large-scale genomics

CuGen is a GPU-accelerated framework for large-scale genomics that enables efficient GWAS and fine-mapping with robust confounding control.

Standing Genomic Variation inferred by popGWAS Predicts Seedling Drought Survival Experiment in Fagus sylvatica

The paper uses popGWAS to identify genomic variation predicting drought survival in Fagus sylvatica seedlings, showing wild-collected material outperforms seed bank sources.

Integrating Genome-Wide Association Analysis, Functional Annotation and Regulatory Genomics for the Prioritization of Candidate Variants Associated with Grain Yield in Upland Rice

This paper identifies genomic variants associated with grain yield in upland rice and develops an integrative framework to prioritize candidate variants by combining GWAS, functional annotation, and regulatory genomics.

Cross-cohort analysis of expression and splicing quantitative trait loci in TOPMed

The paper analyzes expression and splicing quantitative trait loci (e/sQTL) across multiple tissues in the TOPMed dataset and finds that secondary e/sQTL signals are still discoverable, with many GWAS signals colocalizing with these e/sQTL.

High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples

This paper introduces DeepDETAILS, a method to reconstruct cell-type-specific genomic signals from bulk data, outperforming traditional methods and providing insights into disease mechanisms.

Cognitive pleiotropy reveals disorder-specific and shared biology for schizophrenia and bipolar disorder

This paper identifies genetic loci associated with schizophrenia and bipolar disorder using cognitive pleiotropy, revealing shared and disorder-specific biological mechanisms.

Current challenges in GWAS integration and fine-mapping for variant interpretation

This paper identifies challenges in GWAS integration and fine-mapping for variant interpretation and suggests a multi-modal approach for prioritizing causal variants.

Integrating multi-ancestry common and rare variant mapping accelerates therapeutic target discovery

This study integrates common and rare variant mapping across diverse populations to identify novel therapeutic targets, finding NRG4 as a candidate for preserving kidney function.