fine-mapping

Reflection Knockoffs via Householder Reflection: Applications in Proteomics and Genetic Fine Mapping

This paper introduces reflection knockoffs for feature selection in highly correlated datasets, showing improved performance in proteomics and genetic fine mapping.

Genome-wide meta-analysis and integrative fine-mapping identify novel susceptibility loci and effector genes in psoriatic arthritis

This study identifies 40 novel susceptibility loci for psoriatic arthritis through GWAS and fine-mapping, including new therapeutic targets and disease-relevant cell types.

Exploiting pleiotropy to enhance variant discovery with functional false discovery rates

This paper introduces sfFDR to enhance variant discovery by integrating related trait summary statistics, increasing power and discovering additional SNPs in GWAS.

An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome

The paper constructs a bovine epigenomic atlas to annotate regulatory elements and decode the regulatory syntax of the cattle genome, aiding in fine-mapping GWAS loci for complex traits.

Multivariate genome-wide association analysis of quantitative reading skill and dyslexia improves gene discovery

This study uses a multivariate GWAS approach to identify genetic loci associated with reading ability and dyslexia, finding 35 new genome-wide significant loci and estimating SNP heritability at 24%.

fSuSiE enables fine-mapping of QTLs from genome-scale molecular profiles

fSuSiE improves fine-mapping of QTLs by modeling spatial genetic effects on molecular traits, achieving higher resolution in identifying causal variants and their molecular targets.

Genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Swiss Large White pigs

This study uses GWAS and RHM to identify genomic regions associated with protein efficiency and performance traits in pigs, highlighting candidate genes and noncoding RNAs.

Synthetic genomic dissection of enhancer context sensitivity and synergy

The paper identifies context-dependent enhancer synergy in mouse embryonic stem cells, showing that enhancers can significantly boost neighboring DHS activity and that this synergy depends on distance and specific transcription factor sequences.

Rare variants and founder effect in an understudied Quebec population

The paper identifies rare pathogenic variants with higher carrier rates in the Beauce region of Quebec due to a regional founder effect, highlighting the need for fine-scale population structure studies.

A genealogy-based approach for revealing ancestry-specific structures in admixed populations

This paper introduces as-eGRM, a method to reveal ancestry-specific structures in admixed populations by incorporating genealogical trees and local ancestry calls, outperforming existing methods in simulated and empirical datasets.

Procrastination partly reflects an evolutionary byproduct of non-planning impulsivity

The paper shows non-planning impulsivity predicts procrastination and shares genetic overlap, with DLPFC deviations partially explaining this link.

Genetic Architecture and Risk Profile of Alcohol-Related Diseases

This study identifies 93 genetic loci associated with alcohol-related diseases using FinnGen data and shows polygenic risk scores can stratify risk for these diseases and related outcomes.

Tailoring a glycerol-free cryopreservation protocol with anti-freeze (glycol)proteins for commercial and native breeds of chicken

This study evaluates the effects of antifreeze proteins on chicken semen cryopreservation, finding mixed results in post-thaw viability and fertility.

Identification of functional non-coding variants associated with orofacial cleft

This study identifies functional non-coding variants associated with orofacial cleft by combining GWAS, reporter assays, and stem cell modeling.

Borzoi-informed fine mapping improves causal variant prioritization in complex trait GWAS

Sniff improves causal variant prioritization in GWAS by integrating Borzoi-predicted variant effects with functional annotations, identifying more fine-mapped variants with higher posterior inclusion probabilities.

Identification of novel protective loci for executive function using the trail making test part B in the Long Life Family Study

This study identifies novel protective genetic variants associated with TMT-B performance using a family-based GWLS approach in the Long Life Family Study.

Loss of CFHR5 function reduces the risk for age-related macular degeneration

The paper identifies CFHR5 variants that reduce AMD risk by lowering FHR-5 levels and altering complement pathway activity.

Causes and consequences of vascular dementia across the life course: Evidence from a UK Biobank phenome-wide and Mendelian randomization study

This study identifies causes and consequences of vascular dementia using polygenic risk scores, phenome-wide association, and Mendelian randomization analyses from UK Biobank data, highlighting cardiometabolic and educational factors as key modifiable risks.

Genome-wide association studies and multi-omics integrative analysis reveal novel loci and their molecular mechanisms for circulating polyunsaturated, monounsaturated, and saturated fatty acids

The paper identifies novel genetic loci for circulating fatty acids and reveals their molecular mechanisms through GWAS and multi-omics integration.

Genetic diversity and population structure of pedunculate oaks (Quercus robur) in Wytham Woods

This study examines genetic diversity and population structure of pedunculate oaks in Wytham Woods, finding weak population structure and some inbreeding in young plantations.

The Ethnic/Racial Variations of Intracerebral Hemorrhage Genetics (ERICH-GENE) Study Protocol

ERICH-GENE collects and analyzes genomic and neuroimaging data from over 10,000 multi-ethnic ICH cases to identify genetic risk factors and trans-ethnic variation in ICH.

Pleiotropic heritability quantifies the shared genetic variance of common diseases

This paper introduces PHBC to estimate pleiotropic heritability across diseases, finding that about half of common disease heritability is shared with other diseases.

Leveraging molecular-QTL co-association to predict novel disease-associated genetic loci using a graph convolutional neural network

Shared loci but distinct variants underlie genetic architecture of allergic diseases

The paper identifies disease-specific risk variants and shared effector genes in allergic diseases using functional fine-mapping and expression quantitative trait loci.

It's a wrap: deriving distinct discoveries with FDR control after a GWAS pipeline

This paper introduces solveblock, a software tool that enables FDR-controlled conditional independence analysis using GWAS summary statistics, leading to additional discoveries in British individuals.

Comprehensive molecular impact mapping of common and rare variants at GWAS loci

DNACipher predicts variant effects across cell types and assays, identifying imVars at most GWAS loci with support from experimental data.

An application of the MR-Horse method to reduce selection bias in genome-wide association studies of disease progression

The paper applies the MR-Horse method to reduce selection bias in GWAS of disease progression by accounting for genetic correlation and pleiotropy, showing reduced bias and controlled type 1 error rates.

MDA5 variants trade antiviral activity for protection from autoimmune disease

The paper identifies MDA5 variants that protect against autoimmune diseases but increase IBD risk, showing a trade-off between antiviral activity and autoimmunity.

Population genomics for coral reef restoration - a case study of staghorn corals in Micronesia

This study uses population genomics to guide coral reef restoration by analyzing genetic diversity and connectivity in staghorn corals in Micronesia, identifying key populations for conservation and restoration strategies.

Fine-Resolution Asymmetric Migration Estimation

The paper develops an algorithm to estimate asymmetric migration rates in population genetic models and applies it to datasets from poplar trees, gray wolves, and humans, revealing complex migration patterns.