fine-mapping

Assessment of common genetic variation in Alzheimer's and Parkinson's diseases reveals global distinction in population attributable risk

This study assesses genetic variation in Alzheimer's and Parkinson's diseases across ancestries, finding distinct population attributable risks for different loci.

Meta-SAIGE: Scalable and Accurate Meta-Analysis for Rare Variants

Meta-SAIGE improves rare variant meta-analysis by controlling type I error and enhancing computational efficiency, identifying 237 associations across 83 disease phenotypes.

A Genome-wide Association Study Identifies Novel Genetic Variants Associated with Knee Pain in the UK Biobank (N = 441,757)

This paper conducts a GWAS on 441,757 UK Biobank participants to identify genetic variants associated with knee pain, finding 10 significant loci, including eight novel ones, and sex-specific associations.

Allelic effects on KLHL17 expression likely mediated by JunB/D underlie a PDAC GWAS signal at chr1p36.33

The paper fine-maps a PDAC GWAS signal at chr1p36.33 and identifies KLHL17 as a target gene regulated by JunB/D, with potential implications for inflammation and PDAC risk.

Causal interpretations of family GWAS in the presence of heterogeneous effects

This paper shows that family-based GWAS estimates are not generally unbiased for average causal effects but can provide insights into Mendelian segregation's contribution to population-level trait variance.

Integration of GWAS and multi-omic QTLs identifies uncharacterized COVID-19 gene-biotype and phenotype associations

The paper integrates GWAS and multi-omic QTLs to identify gene-biotype and phenotype associations related to COVID-19, revealing pleiotropy and causal links.

Whole genome analysis of plasma fibrinogen reveals population-differentiated genetic regulators with putative liver roles.

This study uses whole genome sequencing to identify 18 novel genetic loci associated with plasma fibrinogen levels, including variants more common in African populations and linked to liver-related traits and disease.

Extensive co-regulation of neighbouring genes complicates the use of eQTLs in target gene prioritisation

The paper benchmarks methods for prioritizing GWAS target genes using eQTLs and finds that assigning pQTLs to closest protein-coding genes outperforms colocalisation methods.

Credible set is sensitive to imputation quality and missing variants

This study shows that credible sets in GWAS are affected by imputation quality and missing variants, and proposes a reweighting method to improve accuracy.

Fine-mapping across diverse ancestries drives the discovery of putative causal variants underlying human complex traits and diseases

This paper introduces SuSiEx, a cross-population fine-mapping method that improves resolution and power by integrating data across ancestries, leading to more accurate identification of causal variants in complex traits and diseases.

The Genetic Determinants and Genomic Consequences of Non-Leukemogenic Somatic Point Mutations

The paper develops a method to quantify somatic mutation burden in whole-genome sequencing data without paired-tissue samples and identifies genetic and phenotypic correlates of clonal hematopoiesis without known driver mutations.

Genetics of posttraumatic stress disorder and cardiovascular conditions using Lifes Essential 8, Electronic Health Records, and Heart Imaging

This study identifies shared genetic loci and genes between PTSD and cardiovascular conditions using GWAS across multiple data sources and finds overlapping biological pathways and drug targets.

Finemap-MiXeR: A variational Bayesian approach for genetic finemapping

Finemap-MiXeR improves genetic finemapping accuracy by using a variational Bayesian approach, outperforming existing methods in synthetic and real data.

Genome-Wide Large-Scale Multi-Trait Analysis Characterizes Global Patterns of Pleiotropy and Unique Trait-Specific Variants

This study identifies pleiotropic variants and trait-specific susceptibility variants using GWAS data from 116 traits, revealing widespread pleiotropy and unique genetic contributions to specific traits.

Diversity and Scale: Genetic Architecture of 2,068 Traits in the VA Million Veteran Program

Population-stratified GWAS of 2,068 traits in 635,969 Million Veteran Program participants, 29% genetically non-European, yields 98,485 associations and 57,601 fine-mapped signals with largely shared cross-population architecture.

Distinct genetic liability profiles define clinically relevant patient strata across common diseases

The paper identifies genetically distinct patient subgroups across diseases by analyzing polygenic risk and pathway convergence.

Strawberry phenotypic plasticity in flowering time is driven by interaction between genetic loci and temperature

The paper identifies temperature-modulated QTL for flowering time plasticity in strawberries and develops a genetic marker for breeding applications.

Discovery of genomic and transcriptomic pleiotropy between kidney function and soluble receptor for advanced glycation end-products using correlated meta-analyses: The Long Life Family Study (LLFS)

The paper identifies pleiotropic genetic factors shared between kidney function and sRAGE using GWAS and TWAS in the LLFS cohort.

Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank

The paper introduces ROH-DICE, a method to identify ROH diplotypes in UK Biobank, finding associations between clustered ROHs and diseases like autoimmune disorders and haemochromatosis.

Fine Mapping and Candidate Gene Analysis of Dravet Syndrome Modifier Loci on Mouse Chromosomes 7 and 8

This study refines two Dravet syndrome modifier loci in mice and identifies candidate genes that may influence disease severity.

Multi-ancestry polygenic risk scores for venous thromboembolism

This study develops multi-ancestry polygenic risk scores for venous thromboembolism using diverse GWAS data and shows improved predictive performance across European- and African-ancestry populations.

Gene regulatory activity associated with PCOS revealed DENND1A-dependent testosterone production

The paper identifies gene regulatory mechanisms in PCOS-associated loci, showing DENND1A-dependent testosterone elevation through experimental and genetic analyses.

Genetic regulation of cell-type specific chromatin accessibility shapes the etiology of brain diseases

The paper identifies cell-type specific chromatin accessibility QTLs and their functional impact on brain disease risk.

Genetic Association and Transferability for Urinary Albumin-Creatinine Ratio as a Marker of Kidney Disease in four Sub-Saharan African Populations and non-continental Individuals of African Ancestry

This study conducts a GWAS on urinary albumin-to-creatinine ratio in Sub-Saharan African and non-resident African-ancestry populations, identifying two genome-wide significant loci and highlighting limited transferability of polygenic scores across populations.

Combining Transdiagnostic and Disorder-Level GWAS Enhances Precision of Psychiatric Genetic Risk Profiles in a Multi-Ancestry Sample

This paper combines transdiagnostic and disorder-level GWAS to enhance genetic risk profiles for psychiatric disorders in multi-ancestry samples, identifying novel SNPs and shared genetic variance.

A fine-scale genetic map of the Japanese population

This paper constructs a fine-scale genetic map of the Japanese population using whole-genome sequencing data, identifies recombination hotspots, and shows improved haplotype phasing and imputation accuracy.

GUIDE deconstructs genetic architectures using association studies

This paper introduces GUIDE, a method to identify latent genetic factors from GWAS data, revealing biological pathways and environmental influences in complex traits.

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

This paper introduces SBayesRC, a method that improves polygenic prediction of complex traits by integrating GWAS summary statistics with functional genomic annotations, showing significant accuracy gains across ancestries.

Genome-wide study of half a million individuals with major depression identifies 697 independent associations, infers causal neuronal subtypes and biological targets for novel pharmacotherapies.

This study identifies 697 genetic associations for major depression using GWAS, infers causal neuronal subtypes, and suggests potential drug targets and repurposing opportunities.

Haplotype Function Score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

The paper introduces Haplotype Function Score (HFS) to improve genetic association analysis and polygenic prediction by replacing genotypes with functional scores, showing increased causal findings and better cross-ancestry prediction.