fine-mapping

High Quality Phasing Using Linked-Read Whole Genome Sequencing of Patient Cohorts Informs Genetic Understanding of Complex Traits

The paper uses linked-read sequencing to phase alleles in 477 CF patients, revealing haplotypes that explain disease mechanisms and contribute to understanding complex traits.

Multiple Causal Variants Underlie Genetic Associations in Humans

This study identifies multiple causal variants underlying genetic associations in humans using MPRA and eQTL data.

Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits - the Hispanic/Latino Anthropometry Consortium

This study identifies novel genetic loci for BMI, height, and WHRadjBMI in Hispanic/Latino populations and shows the benefits of ancestral diversity in GWAS.

FinnGen: Unique genetic insights from combining isolated population and national health register data

Finnish-enriched low-frequency variants, often coding, underlie many GWAS signals across 1,932 register endpoints in 218,792 Finns; a 15-disease meta-analysis with Estonian and UK biobanks adds 30 unreported associations.

Functional non-coding SNPs in human endothelial cells fine-map vascular trait associations

The paper identifies functional non-coding SNPs in human endothelial cells that influence vascular traits by affecting transcriptional regulation and chromatin states.

A multi-dimensional integrative scoring framework for predicting functional variants in the human genome

The paper introduces MACIE, a framework for predicting functional variants by integrating diverse annotations, and applies it to fine-mapping using GWAS data.

An Effector Index to Predict Causal Genes at GWAS Loci

The paper introduces the Effector Index, an algorithm to predict causal genes at GWAS loci using genomic features, achieving 85% AUC in type 2 diabetes validation.

Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast

The paper introduces BB-QTL mapping to study complex traits in yeast, revealing polygenic, pleiotropic, and epistatic genetic architectures with increased sample size.

Partitioning gene-mediated disease heritability without eQTLs

The paper estimates the fraction of disease heritability mediated by genes linked to SNPs without using eQTLs, finding that the closest gene mediates 27% of heritability and some genes outside the top ten also contribute significantly.

Redefining tissue specificity of genetic regulation of gene expression in the presence of allelic heterogeneity

The paper introduces CAFEH, a method to better identify causal regulatory variants across tissues by accounting for allelic heterogeneity and linkage disequilibrium in eQTL data.

Sex differences, cross-ancestry generalizability, and noise-smoking interactions in the polygenic architecture of hearing loss in adults

This study identifies 54 risk loci for hearing loss in adults across multiple cohorts, revealing sex differences, ancestry-specific polygenic risks, and interactions with environmental factors like noise and smoking.

Shared genetic influences on resting-state functional networks of the brain

This study uses a multivariate method to identify shared genetic factors influencing resting-state brain networks and finds nine replicated SNPs associated with their joint architecture.

LMM-MQM time series mapping - An application in a murine advanced intercross line identifies novel growth QTLs

This study uses LMM-MQM time series mapping to identify additional QTLs for body weight in mice, improving the explained variance of a known locus and detecting novel loci.

Epigenomic and transcriptomic prioritization of candidate obesity-risk regulatory GWAS SNPs

The paper prioritizes regulatory SNPs from obesity GWAS by analyzing epigenomic and transcriptomic features in adipose tissue, identifying 47 potential causal SNPs across 14 genes.

A flexible summary-based colocalization method with application to the mucin Cystic Fibrosis lung disease modifier locus

The paper introduces a new colocalization method, SS2, to identify the gene responsible for a CF lung disease locus, finding significant colocalization with MUC4.

Trans-ethnic eQTL meta-analysis of human brain reveals regulatory architecture and candidate causal variants for brain-related traits

The paper performs a trans-ethnic eQTL meta-analysis to identify regulatory variants and candidate causal genes for brain-related traits.

Fine human genetic map based on UK10K data set

This study estimates human recombination rates using the UK10K dataset and shows that larger sample sizes reduce recombination rate fluctuations and improve precision.

Genome-wide Identification of the Genetic Basis of Amyotrophic Lateral Sclerosis

This study identifies 690 candidate ALS genes using a hierarchical Bayesian model, highlighting genetic convergence on the distal axon and functional significance in motor neurons.

Alzheimer's disease variant portal (ADVP): a catalog of genetic findings for Alzheimer's disease

The paper introduces ADVP, a catalog of Alzheimer's disease genetic associations, integrating data from over 200 GWAS publications to provide harmonized and searchable genetic findings.

GWAS and ExWAS of blood Mitochondrial DNA copy number identifies 73 loci and highlights a potential causal role in dementia

This study identifies 73 genetic loci associated with blood mitochondrial DNA copy number and suggests a causal link between low mtDNA-CN and dementia risk.

Genomic and transcriptomic data analyses highlight KPNB1 and MYL4 as novel risk genes for congenital heart disease

The paper identifies KPNB1 and MYL4 as novel risk genes for congenital heart disease through GWAS, eQTL analysis, and functional validation in patient-derived cardiomyocytes.

Educational attainment as a modifier of the effect of polygenic scores for cardiovascular risk factors: cross-sectional and prospective analysis of UK Biobank

This study examines how educational attainment modifies polygenic scores for cardiovascular risk factors using UK Biobank data, finding mixed effects across traits.

Meta-analysis of the genetic loci of pigment pattern evolution in vertebrates

This study meta-analyzes genetic loci associated with vertebrate pigmentation patterns, finding that cis-regulatory mutations are more common in species with diverse pigment cell classes and certain trait types.

Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologies

The paper analyzes the transcriptome of human microglia across brain regions, aging, and disease to identify genetic effects on gene expression and splicing, linking them to neurological disorders.

Trans-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation

This study identifies 277 T2D loci using diverse populations and improves fine-mapping to assess causal genes and mechanisms, enhancing clinical translation.

Fine mapping of goat polledness variant in six Chinese native breeds

The paper identifies a structural variant associated with goat polledness through GWAS and CNV analysis, linking it to the ERG gene and providing insights into its molecular mechanisms.

Genetic diversity patterns of human ethnic groups as inferred from the 1000 genomes

The paper analyzes genetic diversity patterns across human ethnic groups using the 1000 Genomes Project data, identifying group-specific fixed alleles and their evolutionary implications.

The evolutionary genetics of polygenic diseases with the largest global burden in mortality rates

The paper investigates the evolutionary genetics of polygenic diseases with high mortality rates, finding no strong evidence of recent positive selection but evidence of background selection on disease-associated loci across populations.

Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors

This paper introduces DENTIST, a method to reduce errors and heterogeneity in GWAS summary data, improving analyses like COJO and fine-mapping.

Summary statistics knockoff inference empowers identification of putative causal variants in genome-wide association studies

This paper introduces GhostKnockoff, a method to improve causal variant identification in GWAS by increasing statistical power and reducing proxy variants.