fine-mapping

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

The paper performs population-scale single-nucleus multi-omic profiling of skeletal muscle to identify genetic regulation across cell types and traits.

Contrasting levels of transcriptome-wide SNP diversity and decoupled patterns of molecular and functional adaptive variation in conifers

The paper assesses transcriptome-wide SNP diversity and adaptive variation in conifers, finding limited convergence at the molecular level but increased convergence at gene family and biological process levels.

Exome-wide tandem repeats confer large effects on subcortical volumes in UK Biobank participants

The paper identifies exome-wide tandem repeats associated with subcortical volumes and psychiatric symptoms in UK Biobank participants.

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

Rare-variant depletion in 1kb windows of 76,156 gnomAD genomes, versus feature-adjusted mutation expectations, marks regulatory elements and outperforms seven alternative scores at flagging functional non-coding variants.

Polymorphic short tandem repeats make widespread contributions to blood and serum traits

The paper identifies 119 high-confidence STR-trait associations across 93 STRs for blood and serum traits using imputed genotypes from UK Biobank data.

Improving fine-mapping by modeling infinitesimal effects

This paper introduces improved fine-mapping methods that model infinitesimal effects, showing better calibration and increased PRS accuracy for causal variant identification in complex traits.

DYNATE: Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree

DYNATE identifies rare-variant association regions by dynamically aggregating genomic regions and controlling false discovery rate, finding a new ALS-associated gene.

DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants

The paper identifies functional non-coding genetic variants by combining DNase footprints and enhancer RNAs, introducing a framework called FINDER to prioritize variants for functional validation.

Analysis across Taiwan Biobank, Biobank Japan and UK Biobank identifies hundreds of novel loci for 36 quantitative traits

The paper identifies 979 novel genetic loci for 36 quantitative traits by analyzing data from the Taiwan Biobank, Biobank Japan, and UK Biobank, highlighting the value of diverse populations in GWAS.

Leveraging information between multiple population groups and traits improves fine-mapping resolution

This paper introduces MGflashfm and MGfm, methods that improve fine-mapping resolution by integrating multiple traits and population groups using summary statistics.

Genetic Insights into Agronomic and Morphological Traits of Drug-Type Cannabis Revealed by Genome-Wide Association Studies

This study performs GWAS on drug-type Cannabis to identify genetic markers associated with agronomic and morphological traits using HD-GBS and statistical methods.

A benchmark study on current GWAS models in admixed populations

This study benchmarks GWAS models in admixed populations, finding SAIGE has better type-I error control while Tractor excels in detecting ancestry-specific variants but struggles with small samples.

Inferring disease architecture and predictive ability with LDpred2-auto

This paper validates LDpred2-auto for inferring genetic parameters and shows improved heritability capture and predictive performance with an expanded variant set.

Integrated multi-omics single cell atlas of the human retina

The paper creates a comprehensive human retina cell atlas using single-cell multi-omics data, revealing over 110 cell types and their gene regulatory networks, and enables fine-mapping of GWAS and eQTL variants.

Transcriptomics and chromatin accessibility in multiple African population samples

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

Genome-wide Association Identifies Novel Etiological Insights Associated with Parkinsons Disease in African and African Admixed Populations

Intronic GBA1 variant rs3115534-G, common in African and African admixed ancestry but rare elsewhere, raises Parkinson's disease risk (OR 1.58) and lowers onset age.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions

The paper uses CRISPR D-BUGS and chromosome swapping to identify and resolve genetic interactions in synthetic chromosomes, revealing unexpected links between transcription, inositol metabolism, and tRNA abundance.

Genome-wide association analysis of plasma lipidome identifies 495 genetic associations

This study identifies 495 genetic associations with plasma lipid species using genome-wide analysis in 7,174 Finnish individuals and fine-mapping in 377,277 participants, revealing 9 novel loci and disease links.

XMAP: Cross-population fine-mapping by leveraging genetic diversity and accounting for confounding bias

XMAP improves fine-mapping by using cross-population GWAS data and accounting for confounding bias, enhancing statistical power and computational efficiency.

Enrichment of Rare and Uncommon Neanderthal Polymorphisms in Autistic Probands and Siblings

The paper identifies Neanderthal-derived SNPs enriched in autistic probands and siblings, suggesting a role in autism susceptibility across populations.

Data Simulation to Optimize the GWAS Framework in Diverse Populations

This study simulates genomic data from diverse populations to assess GWAS tool performance and proposes an optimized framework for analyzing GWAS data in non-European populations.

A multi-ancestry genome-wide meta-analysis, fine-mapping, and target gene prioritization to characterize the genetic architecture of adiponectin.

This study performs a multi-ancestry GWAS for adiponectin, identifies 22 loci, and prioritizes target genes using GPScore, revealing novel genes and pathways involved in metabolic regulation.

Novel Alzheimer's disease genes and epistasis identified using machine learning GWAS platform

This study identifies novel Alzheimer's disease genes and epistasis using machine learning GWAS tools, capturing more phenotypic variance and discovering new loci with epistatic interactions.

Understanding and Predicting Polycystic Ovary Syndrome through Shared Genetics with Testosterone, SHBG, and Chronic Inflammation

This study identifies genetic loci associated with PCOS and shows genetic correlations with inflammation and sex hormones, improving PCOS prediction through polygenic risk scores.

Nationwide genomic biobank in Mexico unravels demographic history and complex trait architecture from 6,057 individuals

The alpha-2A-adrenergic receptor (ADRA2A) modulates susceptibility to Raynaud's syndrome

This study identifies ADRA2A as a major risk locus for Raynaud's syndrome through genome-wide association analysis and functional validation in vascular smooth muscle cells.

Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study

The paper identifies 83 rare lncRNA variant sets associated with blood lipid levels using WGS data from the TOPMed program and validates some in UK Biobank data.

Multi-ancestry Polygenic Mechanisms of Type 2 Diabetes Elucidate Disease Processes and Clinical Heterogeneity

This study identifies genetic subtypes of type 2 diabetes across diverse ancestries, revealing ancestry-specific risk profiles and BMI thresholds.

High-resolution mapping of Ryd4Hb, a major resistance gene to Barley yellow dwarf virus from Hordeum bulbosum

This study fine-maps the Ryd4Hb resistance gene to a 66.5 kbp interval in barley and dissociates it from a sublethality factor, enabling targeted breeding for BYDV resistance.

Decoding genetic architecture of dog complex traits by constructing fine-scale genomic ancestry of admixture

The paper develops a method to reconstruct fine-scale genomic ancestry in admixed dog breeds and identifies genes associated with body size traits.