fine-mapping

Trans-ancestry genome-wide association study identifies novel genetic mechanisms in rheumatoid arthritis

This study conducts a trans-ancestry GWAS of rheumatoid arthritis, identifying 124 loci, 34 novel, and shows improved polygenic risk score performance across populations.

Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley

This paper uses EnvGWAS and EigenGWAS on historical wheat and barley varieties to identify genomic regions under selection without phenotyping, finding 16 barley and 10 wheat regions with adaptation-related introgressions.

eSCAN: Scan Regulatory Regions for Aggregate Association Testing using Whole Genome Sequencing Data

eSCAN improves aggregate association testing in WGS data by integrating enhancer regions, enhancing statistical power and resolution in blood cell trait analysis.

Prioritising Autoimmunity Risk Variants for Functional Analyses by Fine-Mapping Mutations Under Natural Selection

The paper identifies candidate SNPs under natural selection in autoimmune disorder risk loci and shows they colocalize with selected variants, suggesting functional relevance and implications for autoimmunity.

Causal Haplotype Block Identification in Plant Genome-Wide Association Studies

This paper introduces HapFM, a haplotype-based fine-mapping framework for plant GWAS, which improves mapping power and resolution compared to existing methods.

Integration of GWAS and TWAS to elucidate the genetic architecture of natural variation for leaf cuticular conductance in maize

The paper integrates GWAS and TWAS to identify 22 candidate genes regulating maize leaf cuticular conductance, with ISTL1 validated as a key gene through near-isogenic lines.

Flashfm: A Flexible and Shared Information Fine-mapping Approach for Multiple Quantitative Traits

Flashfm improves fine-mapping of multiple quantitative traits by sharing information between traits, reducing potential causal variants by 20% in a Ugandan cohort.

Leveraging Health Systems Data to Characterize a Large Effect Variant Conferring Risk for Liver Disease in Puerto Ricans

The paper identifies a risk variant for liver disease in Puerto Ricans by integrating EHR and genomic data, showing a dose-dependent association with disease severity.

Evolutionarily conserved clusters of colon with lung cancer susceptibility loci, linked with most DUSP phosphatase genes, may help to dissect mechanisms of cancer susceptibility

The paper identifies evolutionarily conserved genetic clusters linking colon and lung cancer susceptibility loci with DUSP phosphatase genes across species.

Quantitative modeling of fine-scale variations in the Arabidopsis thaliana crossover landscape

The paper develops a predictive model of recombination rates in Arabidopsis thaliana by integrating epigenetic, genomic, and sequence divergence factors.

De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus

This study uses interspecies GWAS to identify candidate genes regulating days to flowering in Amaranthus, revealing homologs of known flowering regulators from Arabidopsis.

A sex-specific evolutionary interaction between ADCY9 and CETP

The paper identifies a sex-specific evolutionary interaction between ADCY9 and CETP variants associated with dalcetrapib response and cardiovascular traits.

Fine-mapping of Parkinson's disease susceptibility loci identifies putative causal variants

This study fine-maps Parkinson's disease susceptibility loci to identify putative causal variants and their mechanisms of action.

Two-phase sample selection strategies for design and analysis in post-genome wide association fine-mapping studies

The paper proposes two-phase sampling strategies for post-GWAS fine-mapping studies to improve power and efficiency while controlling type 1 error.

Replication of LZTFL1 gene region as a susceptibility locus for COVID-19 in Latvian population.

The paper replicates the 3p21.31 locus as a susceptibility locus for COVID-19 in a Latvian population, identifying variants in LZTFL1 associated with increased infection and hospitalization risk.

Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

This study compares genetic variation in synthetic recombinant Saccharomyces cerevisiae populations created by pairwise crossing versus mixing parental strains, finding that crossing increases initial genetic variation and adaptive potential.

Japan COVID-19 Task Force: a nation-wide consortium to elucidate host genetics of COVID-19 pandemic in Japan

The paper reports a genome-wide association study of COVID-19 in a Japanese population, identifying a novel risk variant associated with severe disease in younger patients.

A Chinese host genetic study discovered type I interferons and causality of cholesterol levels and WBC counts on COVID-19 severity

This study identifies cholesterol levels and WBC counts as causal factors for COVID-19 severity through GWAS and MR analysis, and highlights type I interferon pathways in disease mechanisms.

A global atlas of genetic associations of 220 deep phenotypes

Cross-population GWAS of 220 phenotypes in BioBank Japan, UK Biobank, and FinnGen (n=628,000) identifies 5,343 previously unreported loci and decomposes summary statistics into latent genetic components for disease subtyping.

A more accurate method for colocalisation analysis allowing for multiple causal variants

This paper improves colocalisation analysis by integrating the SuSiE framework, enhancing accuracy when multiple causal variants are present.

Investigating the shared genetic architecture between multiple sclerosis and inflammatory bowel diseases

This study investigates genetic correlations and causal relationships between multiple sclerosis and inflammatory bowel diseases, identifying shared SNPs and tissue-specific heritability patterns.

Fine mapping of the HLA locus in Parkinson's disease in Europeans

This study fine maps the association between HLA genes and Parkinson's disease in Europeans, identifying specific amino acid variants in HLA-DRB1 that are protective against PD.

Identifying Causal Variants by Fine Mapping Across Multiple Studies

This paper introduces MsCAVIAR, a method for fine mapping causal variants across multiple GWAS studies, showing it reduces causal set sizes by over 20% in Type 2 Diabetes analysis.

On Cross-ancestry Cancer Polygenic Risk Scores

This study evaluates the utility of breast and prostate cancer polygenic risk scores across different ancestry groups using UK Biobank data, showing significant enrichments in cancer cases within top PRS percentiles.

A meta-analysis of the genome-wide association studies on two genetically correlated phenotypes (self-reported headache and self-reported migraine) identifies four new risk loci for headaches (N=397,385)

This study performs a meta-analysis of GWAS on self-reported headache and migraine, identifying four new risk loci for headaches using 397,385 samples.

Estimating direct and indirect genetic effects on offspring phenotypes using genome-wide summary results data: a comparison of multivariate methods

The paper compares multivariate methods to estimate direct and indirect genetic effects on offspring phenotypes using GWAS summary data, finding Genomic SEM most accurate and identifying novel fertility loci.

echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline

echolocatoR provides an automated pipeline for fine-mapping causal variants using summary statistics and integrates multiple functional genomic datasets.

Insights from complex trait fine-mapping across diverse populations

Fine-mapping 148 complex traits in three biobanks with combined n = 811,261 yields 4,518 causal variant-trait pairs, 285 of them repeating in more than one population.

eQTL Catalogue: a compendium of uniformly processed human gene expression and splicing QTLs

The paper presents the eQTL Catalogue, a resource containing uniformly processed eQTLs from 21 studies, enabling integrative analysis and identification of cell-type-specific eQTLs and disease colocalisations.

Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders

The paper maps open chromatin regions in prenatal human frontal cortex and shows enrichment of SNP heritability for neuropsychiatric disorders within these regions.