fine-mapping

Refining The Accuracy Of Validated Target Identification Through Coding Variant Fine-Mapping In Type 2 Diabetes

This study identifies 16 causal coding variants in type 2 diabetes using fine-mapping and shows that one third of signals are false leads.

Leveraging lung tissue transcriptome to uncover candidate causal genes in COPD genetic associations

The paper identifies 12 novel COPD loci and candidate causal genes using GWAS and lung eQTL data from 129 risk loci.

Genetic correlations among psychiatric and immune-related phenotypes based on genome-wide association data.

The paper investigates genetic correlations between psychiatric and immune-related phenotypes using GWAS summary data, finding significant shared genetic variants.

Shared Polygenicity detection using Elastic Nets: SHARPEN

The paper introduces SHARPEN, an elastic net method to detect shared polygenicity by selecting SNPs involved in overlapping genetic risk loci using GWAS summary data.

Genome-wide analysis yields new loci associating with aortic valve stenosis

This study identifies two new genetic loci associated with aortic valve stenosis through a large genome-wide association study.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.

Discovering patterns of pleiotropy in genome-wide association studies

This paper introduces SAPPHO methods to detect pleiotropy in GWAS by modeling shared patterns of genetic associations, finding 16 additional and 124 novel loci in meta-analysis.

Population Turnover in Remote Oceania Shortly After Initial Settlement

The paper uses ancient DNA analysis to show that Papuan ancestry arrived in Vanuatu around 2400 BP, suggesting multiple waves of migration from Near Oceania.

lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals

The paper introduces lme4qtl, an R package extending lme4 to enable flexible covariance structures and parameter constraints for QTL mapping in genetic studies of related individuals.

Genomic signatures of fine-scale local adaptation in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, behaviour, and immune defence-related genes.

This study identifies genomic regions under local selection in Atlantic salmon linked to sexual maturation, energy homeostasis, behavior, and immune defense genes.

Is this a fake QTL? A short note on analysis of multiple QTL peaks on the same chromosome

The paper proposes a method to identify spurious QTLs by comparing expected test statistic values at putative QTL positions with observed values.

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

The paper introduces a standardized framework for ancestry data representation in genomics studies and applies it to the NHGRI-EBI GWAS Catalog to improve data integration and analysis.

Identifying tissues implicated in Anorexia Nervosa using Transcriptomic Imputation

This paper uses transcriptomic imputation to identify gene-tissue associations linked to Anorexia Nervosa risk, finding significant links in both brain and metabolic tissues.

A robust method to estimate regional polygenic correlation identifies heterogeneity in the shared heritability between complex traits

The paper introduces a method to estimate regional polygenic correlation between complex traits and finds heterogeneity in shared heritability across genomic regions.

Leveraging allele-specific expression to refine fine-mapping for eQTL studies

This paper develops a statistical method that uses allele-specific expression and eQTL data to improve fine-mapping of causal variants for gene expression, achieving higher specificity than eQTL-only approaches.

LiMMBo: a simple, scalable approach for linear mixed models in high-dimensional genetic association studies

LiMMBo enables efficient joint genetic analysis of high-dimensional phenotypes using linear mixed models and bootstrapping, showing power advantages and scalability.

Identification of powdery mildew resistance QTL in Fragaria x ananassa

This study identifies multiple QTL associated with powdery mildew resistance in strawberry, including stable and transient loci, and suggests their use in marker-assisted breeding.

A Comprehensive Reanalysis Of Publicly Available GWAS Datasets Reveals An X Chromosome Rare Regulatory Variant Associated With High Risk For Type 2 Diabetes.

The paper reanalyzes T2D GWAS data to identify a rare X chromosome variant associated with increased T2D risk in males.

SYSTEMATIC ANALYSES OF AUTOSOMAL RECOMBINATION RATES FROM THE 1000 GENOMES PROJECT UNCOVERS THE GLOBAL RECOMBINATION LANDSCAPE IN HUMANS

The paper analyzes recombination rates across 20 human populations using 1000 Genomes Project data to uncover global recombination hotspots and coldspots.

A combined analysis of genetically correlated traits identifies 107 loci associated with intelligence

This study uses MTAG to combine GWAS of education and income with a GWAS of intelligence, identifying 107 loci and 233 genes associated with intelligence.

Fine-mapping of an expanded set of type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

This study fine-maps type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps, identifying 73 variants with >80% posterior probability of association.

Adiposity QTL Adip20 decomposes into at least four loci when dissected using congenic strains

The paper fine-maps a QTL for gonadal adipose depot weight in mice using congenic strains, revealing at least four distinct loci within the original QTL region.

High resolution genetic mapping of causal regulatory interactions in the human genome

This study develops a statistical model to infer causal regulatory interactions using ATAC-seq data and applies it to fine-map eQTL data, reducing credible set size by half.

FUMA: Functional mapping and annotation of genetic associations

FUMA provides a web-based platform for functional annotation of GWAS results, gene prioritization, and interactive visualization using multiple biological databases.

Proper Conditional Analysis in the Presence of Missing Data Identified Novel Independently Associated Low Frequency Variants in Nicotine Dependence Genes

The paper develops a method to handle missing data in genetic meta-analysis, identifying novel low-frequency variants in nicotine dependence genes with improved accuracy.

Comparison of fine-scale recombination maps in fungal plant pathogens reveals dynamic recombination landscapes and intragenic hotspots

This study compares recombination maps in two fungal plant pathogens, finding conserved large-scale patterns but divergent small-scale hotspots, suggesting dynamic recombination landscapes contributing to rapid evolution.

Local genetic correlation gives insights into the shared genetic architecture of complex traits

This paper introduces a method to quantify local genetic correlations between complex traits using GWAS summary data, identifying genomic regions contributing to genetic correlations and inferring causality.

The Multivariate Normal Distribution Framework for Analyzing Association Studies

This paper reviews how the multivariate normal distribution framework can be used to analyze GWAS by accounting for variant correlations, performing association testing, and enabling fine mapping and imputation.

A probabilistic framework to dissect functional cell-type-specific regulatory elements and risk loci underlying the genetics of complex traits

The paper introduces a probabilistic framework to identify cell-type-specific regulatory elements and risk variants associated with complex traits using epigenomic data.

Evidence of population specific selection inferred from 289 genome sequences of Nilo-Saharan and Niger-Congo linguistic groups in Africa

The paper analyzes 289 genome sequences from Nilo-Saharan and Niger-Congo populations to identify population-specific selection signatures linked to disease resistance.