fine-mapping

Focus on single gene effects limits discovery and interpretation of complex trait-associated variants

The paper introduces a multi-gene eQTL mapping framework to detect variants influencing multiple neighboring genes, finding novel loci and improving colocalization with GWAS variants.

Wild genes to the rescue: High-throughput genomics uncovers the wild source of broomrape resistance in sunflower

This study uses high-throughput genomics to identify wild sunflower relatives as sources of broomrape resistance genes.

SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders

SingleBrain integrates snRNA-seq and genotype data to map cis-eQTLs across brain cell types, identifying novel disease-associated genes and causal variants.

The Impact of Stability Considerations on Genetic Fine-Mapping

This paper introduces a stability-guided fine-mapping approach that complements residualization, showing it enhances functional variant identification in eQTL analysis.

Genetic architecture and functional consequences of lateral root length in maize (Zea mays L.)

The paper identifies QTL for lateral root length in maize across developmental stages and examines their correlation with biomass under different nutrient conditions.

Integrative screening identifies functional variants and VNTRs underlying GWAS signals at the 5p15.33 multi-cancer susceptibility locus

The paper identifies functional variants and VNTRs at the 5p15.33 locus using fine-mapping, MPRA, and CRISPRi screens, revealing their role in cancer susceptibility through antagonistic pleiotropy.

Massively parallel functional profiling identifies CCDC88C as a risk gene for ER-positive breast cancer

The paper identifies CCDC88C as a risk gene for ER-positive breast cancer by analyzing functional variants from GWAS signals using a massively parallel reporter assay.

Fine-scale structure of a whole regional population through genetics and genealogies

This study reveals fine-scale genetic structure in the Saguenay-Lac-Saint-Jean region using genotype data and genealogies, showing a genetic gradient and historical migration patterns.

Genetic correlation analysis identifies TMEM106B, ACE, and ERC2 as genetic loci shared between Alzheimer's disease and primary psychiatric disorders

Sex-specific Genetic Regulatory Effects in Chickens

The paper identifies sex-specific genetic regulatory effects in chickens using whole-genome sequencing and transcriptomes, revealing sex-dependent gene regulation and structural variants.

Population genomics reveals fine-scale three-dimensional structure within two sympatric Sebastes species in the Northwest Atlantic

This study uses population genomics to reveal fine-scale three-dimensional structure in two sympatric Sebastes species in the Northwest Atlantic, highlighting management implications.

Shared genetic factors between lung function and asthma by age at onset

This study identifies shared genetic factors between asthma and lung function that vary by age-at-onset, highlighting distinct mechanisms for early-onset asthma.

Quantifying annotation-stratified pleiotropy and co-polygenicity between complex traits

This paper introduces SBayesAPP, a Bayesian model that estimates annotation-stratified pleiotropy and co-polygenicity between complex traits using GWAS summary statistics, revealing cell-type-specific genetic correlations.

Functional dissection of complex and molecular trait variants at single nucleotide resolution

This study functionally characterizes 221,412 trait-associated variants using MPRA in 5 cell types, identifying 12,025 regulatory variants and revealing widespread epistasis and non-TF mechanisms.

Multi-tissue transcriptome-wide association study identifies 29 risk genes associated with attention-deficit/hyperactivity disorder

This study uses a multi-tissue transcriptome-wide association study to identify 29 risk genes for ADHD, including six previously unlinked genes.

Short tandem repeats significantly contribute to the genetic architecture of metabolic and sensory age-related hearing loss phenotypes

The paper investigates the contribution of short tandem repeats (STRs) to age-related hearing loss phenotypes, finding they explain some missing heritability and identify risk associations.

Development of a Flex-Seq SNP panel for raspberry (Rubus idaeus L.) and validation through linkage map construction and identification of QTL for several traits of agronomic importance to raspberry breeding

The paper develops a Flex-Seq SNP panel for red raspberry and validates it through linkage maps and QTL identification for agronomic traits.

OmiGA: A Toolkit for Ultra-efficient Molecular Trait Analysis in Complex Populations

OmiGA improves molQTL mapping in complex populations by using an efficient linear mixed model, enhancing power and reducing false positives.

Functional characterization of the 9q34.13 locus identifies RAPGEF1 as modulating risk for melanoma and nevi via RAS activation

This study identifies RAPGEF1 as a gene modulating melanoma and nevi risk through RAS activation, using fine-mapping, expression data, and functional assays.

Genomic insights into substance use and disinhibitory disorders

This study identifies 1,294 genomic regions and 961 effector genes associated with externalizing disorders, revealing neural mechanisms and polygenic predictors of variance in these conditions.

The Gene Expression Landscape of Disease Genes

The paper analyses gene expression of disease-associated genes across 46 tissues and 204 cell types to identify their expression patterns in relation to 11 diseases and cancers.

Practical utility of sequence-to-omics models for improving the reproducibility of genetic fine-mapping

This study evaluates sequence-to-omics models to improve reproducibility in genetic fine-mapping across eQTL datasets, showing reduced replication failure rates and enhanced SNP prioritization.

PAD-associated genetic variants are more strongly associated with surgical intervention than premature onset

This study identifies PAD-associated SNPs with stronger associations with surgical intervention than premature onset using UK Biobank data.

Transcriptome-wide association study and fly experiments uncover the role of CoA synthase in ageing across species.

The paper performs a transcriptome-wide association study on human lifespan and validates findings in Drosophila, identifying COASY as a gene involved in ageing across species.

Multi-ancestry conditional and joint analysis (Manc-COJO) applied to GWAS summary statistics

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.

Fast and flexible joint fine-mapping of multiple traits via the Sum of Single Effects model

The paper introduces mvSuSiE, a multi-trait fine-mapping method that improves causal SNP identification by jointly analyzing multiple traits, discovering more causal SNPs and narrower credible sets compared to single-trait approaches.

Integrating multi-omics and multi-context QTL data with GWAS reveals the genetic architecture of complex traits and improves the discovery of risk genes

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.

Prime-InDel version 1: A web tool providing InDel markers for targeted regions narrowing

Prime-InDel provides PCR-based InDel markers for fine-mapping in rice, narrowing QTL intervals effectively.

Utility of polygenic risk scores in diagnostic genetic testing for dilated cardiomyopathy

This study evaluates polygenic risk scores (PRS) in dilated cardiomyopathy (DCM) patients, finding higher PRS in those without monogenic variants and TTN-related DCM, suggesting polygenic contributions.

Per-allele disease and complex trait effect sizes are predominantly African MAF-dependent in European populations

The paper shows that per-allele effect sizes of genetic variants in European populations are better predicted by African MAF than European MAF.