fine-mapping

Improving the coverage of credible sets in Bayesian genetic fine-mapping

This paper improves the resolution of Bayesian genetic fine-mapping by correcting coverage estimates of credible sets, reducing the number of variants to consider in 27 type 1 diabetes regions.

Leveraging mouse chromatin data for heritabilityenrichment informs common disease architecture andreveals cortical layer contributions to schizophrenia

The paper uses mouse chromatin data to identify heritability enrichment in schizophrenia and other diseases, revealing contributions from specific cortical layers and cell types.

The nonlinear structure of linkage disequilibrium

The paper demonstrates the shift between linear and nonlinear dependence in linkage disequilibrium and shows how r2 values can have different implications based on this structure.

Deciphering sex-specific genetic architectures using local Bayesian regressions

This paper develops a local Bayesian regression method to detect sex-specific genetic interactions in complex traits, finding many new interactions with small effects.

Fine-mapping and QTL tissue-sharing information improve causal gene identification and transcriptome prediction performance

The paper improves causal gene identification and transcriptome prediction by integrating fine-mapping and QTL tissue-sharing information into transcriptomic imputation models.

Population histories of the United States revealed through fine-scale migration and haplotype analysis

This study uses genetic and geographic data to analyze migration patterns and population structure in the US, revealing substructure and demographic history among different groups.

Choosing the optimal population for a genome-wide association study: a simulation using whole-genome sequences from rice

This study shows that combining target populations with more diverse populations improves GWAS power for detecting QTNs, depending on genetic diversity metrics like FST and He.

Genome-wide association and multi-omic analyses reveal new mechanisms for Heart Failure

This study identifies one known and two novel genetic variants associated with heart failure through GWAS and multi-omic analyses, revealing potential causal mechanisms and shared heritability with musculoskeletal traits.

Multi-resolution localization of causal variants across the genome

KnockoffZoom identifies causal variants for complex traits at multiple resolutions using artificial genotypes and linkage disequilibrium models, outperforming mixed effects models in the UK Biobank.

RLP/K enrichment sequencing; a novel method to identify receptor-like protein (RLP) and receptor-like kinase (RLK) genes

This paper introduces RLP/KSeq, a method to rapidly map receptor-like protein (RLP) and receptor-like kinase (RLK) genes in plants, demonstrating its application in identifying PRRs in Solanum species.

Allele-Specific QTL Fine-Mapping with PLASMA

PLASMA improves QTL fine-mapping by integrating allele-specific QTL information, achieving better resolution and smaller credible sets than existing methods.

Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype

The paper uses BSA-exome-seq to fine-map the ERA8 mutant in wheat to the TaMKK3-A locus, identifying a missense mutation linked to ABA hypersensitive germination.

Deep learning models predict regulatory variants in pancreatic islets and refine type 2 diabetes association signals

The paper uses deep learning models to predict regulatory variants in pancreatic islets and refines T2D association signals by integrating epigenomic data with genetic fine-mapping.

Fine-mapping of SNCA in REM sleep behavior disorder and overt synucleinopathies

This study identifies SNCA risk variants specific to RBD and overt synucleinopathies, finding distinct associations and opposite effects at the 3' end of SNCA.

Osteoporosis- and obesity-risk interrelationships: An epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15

The paper identifies regulatory SNPs in TBX15 that influence both obesity and osteoporosis risk through epigenetic and genetic analysis of GWAS data.

Genome-wide association study in two cohorts from a multi-generational mouse advanced intercross line highlights the difficulty of replication

This study investigates replication challenges in GWAS using two mouse cohorts, finding limited replication success despite similar sample sizes and population origins.

Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels

This study identifies 11 genetic loci associated with salivary metabolites in 1,419 individuals, revealing novel saliva-specific associations and potential clinical applications.

Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for twelve immune-mediated diseases

This study uses regulatory QTLs from immune cells to fine-map causal variants for twelve immune-mediated diseases, finding smaller credible sets and higher posterior probabilities compared to traditional methods.

GWAS and Fine-Mapping of Livability and Six Disease Traits in Holstein Cattle

The paper performs GWAS and fine-mapping on seven health traits in Holstein cattle to identify genetic variants and candidate genes associated with health outcomes.

A scalable method for estimating the regional polygenicity of complex traits

This paper introduces BEAVR, a scalable method to estimate regional polygenicity using GWAS effect sizes and LD information, showing it provides unbiased estimates compared to existing methods.

Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes

This study fine-maps 150 breast cancer risk regions to identify 178 high confidence target genes using genomic and functional annotations.

GxEMM: Extending linear mixed models to general gene-environment interactions

This paper introduces GxEMM, a mixed model for gene-environment interactions, showing it improves heritability estimates and reveals stress reduces heritability of major depression.

Genetic meta-analysis of obsessive-compulsive disorder and self-report compulsive symptoms.

This paper investigates genetic correlations between compulsive symptoms and OCD using GWAS and finds novel genes and increased enrichment for brain-related genes when combining symptom data with case-control studies.

A Comprehensive Genome-wide and Phenome-wide Examination of BMI and Obesity in a Northern Nevadan Cohort

This study uses EHR and genetics to perform GWAS and PheWAS on BMI and obesity, identifying known and novel variants and phenotypic associations.

Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa.

This study identifies QTLs associated with cellulose saccharification and glucose fermentation in Neurospora crassa using QTL analysis.

Major QTLs for seedling traits in barley using a DArT-based linkage map

This study identifies 46 QTLs for seedling vigour traits in barley using a DArT-based linkage map, with pleiotropic QTLs linked to marker-assisted selection.

Leveraging Family History in Case-Control Analyses of Rare Variation

This paper introduces a new rare-variant association test that incorporates family history information, showing improved performance over standard methods in simulated data and a study of cleft lip and palate.

Pervasive lesion segregation shapes cancer genome evolution

This study shows that DNA lesions segregate between daughter cells, leading to chromosome-scale mutation phasing and increased genetic diversity in cancer genomes.

Population-specific recombination maps from segments of identity by descent

The paper develops a method to estimate population-specific recombination maps using identity by descent segments, showing improved accuracy in European and African American populations compared to existing maps.

High resolution mapping of a Hordeum bulbosum-derived powdery mildew resistance locus in barley using distinct homologous introgression lines

This study fine-maps a powdery mildew resistance gene from Hordeum bulbosum in barley using introgression lines and high-throughput genotyping.