fine-mapping

A joint transcriptome-wide association study across multiple tissues identifies new candidate susceptibility genes for breast cancer

This study performs a joint transcriptome-wide association study across multiple tissues to identify new candidate susceptibility genes for breast cancer, finding 380 genes at 129 loci with 22 remaining significant after conditioning on known variants.

The power of TOPMed imputation for the discovery of Latino enriched rare variants associated with type 2 diabetes

The paper demonstrates that TOPMed imputation improves the identification of rare variants associated with type 2 diabetes in Latino populations, leading to novel associations and better polygenic scores.

Multi-trait genome-wide association analyses leveraging alcohol use disorder findings identify novel loci for smoking behaviors in the Million Veteran Program

This study uses multi-trait analysis to identify novel genetic loci for smoking behaviors by leveraging alcohol use disorder GWAS data from the Million Veteran Program.

Evolutionary Insights from a Large-scale Survey of Population-genomic Variation

This study analyzes population-genomic variation in Daphnia pulex to reveal evolutionary-genomic features and identify genes under selection.

Antithrombin, protein C and protein S: Genome and transcriptome wide association studies identify 7 novel loci regulating plasma levels

Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.

The paper imputes Pictish genomes and analyzes their genetic relationships with ancient and modern UK populations, revealing continuity and structure.

Using brain cell-type-specific protein interactomes to interpret genetic data in schizophrenia

The paper uses brain cell-type-specific protein interactomes to interpret genetic data in schizophrenia and identifies enriched networks and genes associated with the disease.

Population genetic structure of the maize weevil, Sitophilus zeamais, in southern Mexico

This study finds significant genetic population structure in maize weevils from southern Mexico using genome-wide SNP data, suggesting local factors shape genetic differentiation.

Analysis of genetic dominance in the UK Biobank

The paper evaluates dominance effects in over 1,000 UK Biobank phenotypes using GWAS, finding no significant dominance contribution to phenotypic variance from common variation.

Novel insight into the etiology of ischemic stroke gained by integrative transcriptome-wide association study

This study identifies 136 genes/eRNA/proteins associated with ischemic stroke risk using integrative transcriptome-wide association analysis across multiple tissues and finds potential therapeutic candidates.

Deletion mapping of regulatory elements for GATA3 reveals a distal T helper 2 cell enhancer involved in allergic diseases

The paper identifies a distal enhancer for GATA3 involved in allergic diseases by combining GWAS signals with deletion mapping in T helper 2 cells.

A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics

FactorGo identifies pleiotropic components across thousands of human diseases and traits using GWAS summary statistics, outperforming existing methods in capturing latent factors.

flashfmZoom: a tool for joint fine-mapping and exploration of GWAS results in the UK Biobank

flashfmZoom is an R Shiny app that enables joint fine-mapping and exploration of GWAS results from the UK Biobank to identify shared or distinct causal variants across traits.

Validity of European-centric derived cardiometabolic polygenic risk scores in multi-ancestry populations

This study evaluates the performance of European-derived polygenic risk scores for cardiometabolic traits in multi-ancestry populations, finding better performance in Europeans than in South Asians and African Caribbeans.

The lingering effects of Neanderthal introgression on human complex traits

This study assesses the contribution of Neanderthal introgression to human complex traits using UK Biobank data, finding significant but depleted effects compared to modern human variants.

A single base pair duplication in SLC33A1 gene causes fetal losses and neonatal lethality in Manech Tete Rousse dairy sheep

The paper identifies a single base pair duplication in SLC33A1 causing fetal losses and neonatal lethality in MTR sheep through whole genome sequencing and breeding studies.

Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.

This study identifies 43 genomic loci associated with reproductive success in 785,604 individuals, showing ongoing natural selection at the FADS locus.

A Unifying Statistical Framework to Discover Disease Genes from GWAS

This paper introduces a statistical framework to identify disease genes from GWAS by computing gene-level causal variant probabilities, outperforming existing methods and discovering novel disease genes.

Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease

This study identifies causal genetic variants for cardiac traits by integrating spatiotemporal eQTL analysis with GWAS data, showing stage- and tissue-specific effects.

The Genetic and Evolutionary Basis of Gene Expression Variation in East Africans

This study maps expression and splicing QTLs in East Africans and finds population-specific genetic variation related to immunity, metabolism, and pigmentation.

Desynapsis in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility

This paper identifies StMSH4 mutations as the cause of desynapsis in potato, leading to either sterility or uniform unreduced pollen, and shows these alleles are common in cultivars.

Genetic correlates of vitamin D-binding protein and 25 hydroxyvitamin D in neonatal dried blood spots

This study identifies genetic loci associated with vitamin D-binding protein and 25 hydroxyvitamin D in neonates and links DBP to vitamin D status and disease risk.

eXclusionarY: Ten years later, where are the sex chromosomes in GWAS?

The paper re-evaluates the inclusion of sex chromosomes in GWAS, finding persistent underrepresentation and proposing recommendations for improvement.

Automatic detection of complex structural genome variation across world populations

The paper develops a method to detect complex structural variants across human genomes and finds they are associated with phenotypic hotspots and evolutionary changes.

Impact of cross-ancestry genetic architecture on GWAS in admixed populations

This paper quantifies how differences in allelic effect sizes across ancestry backgrounds impact GWAS power in admixed populations and finds modeling these differences does not significantly improve results.

Detecting and Adjusting for Hidden Biases due to Phenotype Misclassification in Genome-Wide Association Studies

This paper introduces PheMED, a tool to quantify effect size dilution in GWAS due to phenotypic misclassification, and demonstrates its applications in improving meta-analysis.

Differentiated genomic footprints and connections inferred from 440 Hmong-Mien genomes suggest their isolation and long-distance migration

This study analyzes 440 Hmong-Mien genomes to reveal genetic differentiation, admixture, and migration patterns, supporting isolation and long-distance migration.

mBAT-combo: a more powerful test to detect gene-trait associations from GWAS data

mBAT-combo improves gene-trait association detection in GWAS by accounting for SNP effect directions, revealing masking effects in complex traits.

Fine-Mapping and Credible Set Construction using a Multipopulation Joint Analysis of Marginal Summary Statistics from Genome-wide Association Studies

This paper introduces mJAM, a multi-population fine-mapping method that improves credible set construction by incorporating population-specific LD structures and demonstrates its effectiveness in real GWAS data.

DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network

DeepGWAS enhances GWAS signals for neuropsychiatric disorders using deep neural networks, improving locus detection in schizophrenia and validating results in other disorders.