fine-mapping

Identification of a core module for bone mineral density through the integration of a co-expression network and GWAS data

The paper identifies a core gene module for bone mineral density by integrating co-expression networks and GWAS data, revealing four novel causal genes.

Genome-wide maps of enhancer regulation connect risk variants to disease genes

The paper uses the ABC Model to map enhancer-gene regulation across 131 cell types and tissues, linking GWAS variants to disease genes, particularly in IBD.

The Parkinson's Disease GWAS Locus Browser

The paper presents a GWAS locus browser for Parkinson's disease that helps prioritize genes associated with risk variants from multiple GWAS studies.

A bHLH transcription factor (VfTT8) underlies zt2, the locus determining zero tannin content in faba bean (Vicia faba L.)

The paper identifies VfTT8, a bHLH transcription factor, as the gene responsible for the zt2 locus controlling zero tannin content and white flower color in faba bean.

Genome-wide mapping and prediction of plant architecture in a sorghum nested association mapping population

The paper identifies quantitative trait loci (QTL) for plant architecture traits in sorghum using a nested association mapping population and evaluates genomic prediction accuracy.

Regulatory signatures of drought response in stress resilient Sorghum bicolor

This study identifies drought-inducible regulatory modules in sorghum by integrating chromatin accessibility and transcriptional data, linking them to water use efficiency variation across genetic diversity.

Enhanced Brain Imaging Genetics in UK Biobank

The paper expands genetic associations with brain imaging phenotypes using updated UK Biobank data, finding more genetic variants and associations, including on the X chromosome.

The Trans-Ancestral Genomic Architecture of Glycaemic Traits

This study identifies 242 genetic loci for glycaemic traits using trans-ancestry meta-analysis, finding 99 novel loci and improved fine-mapping resolution compared to single-ancestry analyses.

Compositional knockoff filter for high-dimensional regression analysis of microbiome data

The paper introduces a compositional knockoff filter to control false discovery rate in high-dimensional microbiome regression analysis, demonstrating improved power while maintaining FDR control.

An ancient deletion in the ABO gene affects the composition of the porcine microbiome by altering intestinal N-acetyl-galactosamine concentrations

A simple new approach to variable selection in regression, with application to genetic fine-mapping

SuSiE writes sparse regression coefficients as a sum of single-effect vectors; its IBSS algorithm returns a credible set per effect and outperformed existing fine-mapping methods in numerical experiments.

Fine-scale Population Structure and Demographic History of Han Chinese Inferred from Haplotype Network of 111,000 Genomes

The paper constructs a haplotype network of 111,000 Han Chinese genomes to reveal fine-scale population structure and demographic history, identifying subclusters linked to geography, immigration, and cultural-linguistic factors.

Geographic patterns of human allele frequency variation: a variant-centric perspective

The paper presents a variant-centric visualization of human genetic variation, revealing geographic patterns and clarifying misconceptions about genetic differentiation.

Design of Experiments for Fine-Mapping Quantitative Trait Loci in Livestock Populations

The paper designs experiments for fine-mapping quantitative trait loci in livestock populations, showing that optimal sample size depends on heritability and the number of causative variants.

Integration of genetic, transcriptomic, and clinical data provides insight into 16p11.2 and 22q11.2 CNV genes

The paper integrates genetic, transcriptomic, and clinical data to identify CNV gene associations with brain-related and health traits, finding pleiotropy and multigenicity in CNV biology.

Analysis of overlapping genetic association in type 1 and type 2 diabetes

This paper identifies four genetic regions associated with both type 1 and type 2 diabetes, with three showing opposite effect directions and one showing concordant effects.

Estimation of Non-null SNP Effect Size Distributions Enables the Detection of Enriched Genes Underlying Complex Traits

The paper introduces gene-ε, a method to detect enriched genes underlying complex traits by improving SNP effect size estimation and reducing false positives in genome-wide association studies.

Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm

This study uses NLP to identify diverticular disease from EHRs and performs GWAS and PheWAS across multiple ancestries to find genetic risk variants and clinical associations.

Predicting Geographic Location From Genetic Variation with Deep Neural Networks

The paper introduces a deep learning method called Locator to predict geographic locations from genetic variation, achieving high accuracy and speed across different species.

Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes

The paper identifies 166 dispensable human genes with common loss-of-function variants that show relaxed selective constraints and some evidence of positive selection.

Lack of evidence for genetic association of saposins A, B, C and D with Parkinson disease

The paper examines genetic associations of saposins A, B, C, and D with Parkinson's disease using SKAT-O and GWAS analyses, finding no significant associations.

Localizing components of shared transethnic genetic architecture of complex traits from GWAS summary data

The paper estimates population-specific and shared causal SNPs from GWAS summary data across East Asian and European populations and finds shared SNPs are enriched in functional categories.

Analysis of putative cis-regulatory elements regulating blood pressure variation

The paper identifies putative cis-regulatory elements associated with blood pressure traits using open chromatin and gene expression data, and identifies several candidate genes for further functional testing.

A custom genotyping array reveals population-level heterogeneity for the genetic risks of prostate cancer and other cancers in Africa

The paper develops a genotyping array tailored for African populations to identify cancer risk variants, finding population-specific allele frequency differences and lower prostate cancer risk in Senegal compared to Nigeria.

Phage-DMS: a comprehensive method for fine mapping of antibody epitopes

Phage-DMS combines immunoprecipitation of phage peptide libraries with deep mutational scanning to fine map antibody epitopes, refining known epitopes for HIV monoclonal antibodies.

Shared genetic etiology between obsessive-compulsive disorder, obsessive-compulsive symptoms in the population, and insulin signaling

The paper identifies shared genetic risk factors between OCD, population-based OCS, and insulin signaling traits, suggesting a common etiological mechanism.

Increasing the resolution and precision of psychiatric GWAS by re-imputing summary statistics using a large, diverse reference panel

This paper improves psychiatric GWAS by re-imputing summary statistics using a larger, more diverse reference panel, revealing new signals from rare variants.

Population genetics of sugar kelp in the Northwest Atlantic region using genome-wide markers

This study analyzes the population genetics of sugar kelp in the Northwest Atlantic using genome-wide markers to assess genetic diversity and detect selection signatures.

Eliciting priors and relaxing the single causal variant assumption in colocalisationanalyses

The paper improves the colocalisation analysis method by introducing data-driven priors and relaxing the single causal variant assumption, enhancing inference robustness and flexibility.

A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene

The paper maps the Yr7 yellow rust resistance gene in wheat using QTL mapping, association mapping, and mapping-by-sequencing, narrowing the interval to a candidate gene.