fine-mapping

Fine-mapping methods for complex traits: essential adaptations for samples of related individuals

This paper introduces Bayesian fine-mapping methods adapted for related individuals, showing improved accuracy in pig data compared to existing tools.

Inferring fine-scale mutation and recombination rate maps in aye-ayes (Daubentonia madagascariensis)

This study infers fine-scale mutation and recombination rate maps in aye-ayes using genomic data, finding lower rates compared to other primates.

CONSILIENCE-GWAS: A Web Resource for Parsed Heritability & Polygenic Score Analysis of Human GWAS Using Heterogeneous Functional Genomics Data

CONSILIENCE-GWAS integrates functional genomics data with human GWAS to analyze heritability and polygenic scores across species.

Iterative improvement of deep learning models using synthetic regulatory genomics

The paper fine-tunes the Enformer model using synthetic regulatory sequences to improve its predictive performance on non-reference sequences.

Genome-wide association and gene-virus interaction study of liver disease in hepatitis C virus-infected patients

This study identifies genetic risk factors and host-viral interactions for cirrhosis progression in hepatitis C virus-infected patients but finds no genome-wide significant associations for hepatocellular carcinoma.

Long-read genome sequencing and multi-omics in aging and neurodegeneration

The paper uses long-read genome sequencing and multi-omics data to identify structural variants associated with aging and neurodegenerative diseases, finding that SVs are more likely to be causal than SNVs.

Large-Scale Gene-Smoking Interactions and Fine Mapping Study Identifies Multiple Novel Blood Pressure Loci in over 1 Million Individuals

This study identifies twelve novel blood pressure loci and shows smoking modifies genetic effects on BP through immune-related pathways in over 1 million individuals.

Cross-ancestral GWAS identifies 29 novel variants across Head and Neck Cancer subsites

This study conducts a cross-ancestral GWAS and fine mapping of head and neck squamous cell carcinoma subsites, identifying 29 novel variants and highlighting gene-environment interactions.

Formal Statistical Replication Analysis in Lung Cancer Genome-Wide Association Studies

This paper introduces a formal statistical replication analysis to reduce false positives in lung cancer GWAS, finding it significantly lowers false discovery rate and improves polygenic risk score efficiency.

Population-scale Long-read Sequencing in the All of Us Research Program

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

A versatile data repository for GWAS summary statistics-based downstream genomic analysis of human complex traits

The paper introduces gact, an R package that integrates GWAS summary statistics with genomic resources to identify causal genes and pathways, demonstrating its application in coronary artery disease and type 2 diabetes.

Genome-wide association study of susceptibility to acute respiratory distress syndrome

This study identifies a genome-wide significant variant associated with sepsis-associated ARDS risk, linking cholesterol metabolism to ARDS susceptibility.

SAFE-LD: A novel method for the estimation of linkage disequilibrium from summary statistics

SAFE-LD estimates linkage disequilibrium from GWAS summary statistics using pseudo-genotypes that preserve in-sample LD while protecting privacy.

MACHINE: a robust and scalable multi-ancestry fine-mapping method using a continuous global-local shrinkage prior

MACHINE improves multi-ancestry fine-mapping by using a continuous prior and FDR control, identifying new causal variants in lipid traits and schizophrenia.

High-density genome-wide association study points out major candidate genes for resistance to infectious pancreatic necrosis in rainbow trout

This study identifies candidate genes for IPN resistance in rainbow trout using a high-density genome-wide association study and Bayesian modeling.

Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk

The paper maps genetic effects on splicing in 10,725 brain samples, identifying 68,358 cis-sQTLs and 97 loci where splicing mediates neurological disease risk.

Disentangling osteoarthritis-specific genetic effects from obesity to identify novel therapeutic targets

This study identifies OA-specific genetic effects and novel therapeutic targets by separating OA genetics from those shared with obesity using GWAS and proteomics data.

Multi-ancestry genome-wide and transcriptome-wide association analyses identify new risk loci and genes for inflammatory bowel disease

This study identifies 60 new susceptibility loci and 441 candidate risk genes for inflammatory bowel disease through multi-ancestry GWAS and TWAS, with implications for precision medicine.

A century of breeding has preserved genetic variation, accumulated favorable alleles, and shaped the Rht gene portfolio in North American spring wheat

This study analyzes genetic diversity and Rht gene changes in North American spring wheat over a century, showing shifts in allele frequencies and their impact on plant height.

Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models

This paper introduces GPN-Star, a phylogeny-informed genomic language model that improves variant effect prediction across species and evolutionary timescales.

Biobank-scale Bayesian TWAS reveals splicing-mediated mechanisms of complex disease

The paper uses Bayesian TWAS to identify splicing-disease associations across multiple cohorts, revealing causal mechanisms in immune, vascular, and metabolic traits.

Systematic assessment of homology-based methods for fine-grained functional annotation using diverse protein families

The paper evaluates BLASTp and profile HMMs for fine-grained functional annotation, finding BLASTp struggles with remote homologs while HMMs improve sensitivity but may miss some family members due to functional divergence.

Protein tyrosine phosphatase receptor type D - A convergent risk gene for MDD, BPD, and ADHD and regulator of dopaminergic neuroplasticity in reward associated circuits; A multivariate GWAS, brain tissue and cell type enrichment, and gene finemapping

This study identifies PTPRD as a shared risk gene for MDD, BPD, and ADHD through multivariate GWAS and proposes a mechanistic role in dopaminergic neuroplasticity.

The Genetic Relationships Between Post-Traumatic Stress Disorder and Its Corresponding Neural Circuit Structures

This study identifies genetic links between PTSD and brain circuitry traits using GWAS meta-analysis and multiple genetic methods, finding shared loci and causal relationships.

Integrative Mendelian Randomization for Detecting Exposure-by-group Interactions Using Group-Specific and Combined Summary Statistics

The paper introduces int2MR, a Mendelian randomization method for detecting exposure-by-group interactions using GWAS summary statistics, showing its effectiveness in identifying sex- and age-group-specific risk factors for ADHD and Alzheimer's disease.

Integrative Gene-Centric Analysis of Breast Cancer: High-Confidence Germline Predisposition Genes from Population-Scale Cohorts

The paper identifies high-confidence breast cancer predisposition genes using multi-ethnic genomic data and integrates GWAS, TWAS, and PWAS to refine the genetic architecture of heritable breast cancer.

Genome-wide associations of fitness components reveal antagonistic pleiotropy and sexual conflict in the Florida Scrub-Jay

The paper identifies genetic trade-offs and antagonistic pleiotropy in Florida Scrub-Jays by analyzing fitness components and their genomic associations.

Common Genetic Variants Modify Disease Risk and Clinical Presentation in Monogenic Diabetes

The paper shows that common genetic variants influence disease risk and severity in monogenic diabetes, modifying clinical outcomes in individuals with pathogenic variants.

Variable information across SNPs in GWAS data can cause false rejections of colocalisation which can be resolved by proportional colocalisation tests

The paper shows that variable information across SNPs in GWAS data can lead to false colocalisation inferences and proposes a proportional colocalisation test to address this issue.

A single nucleotide polymorphism genotyping panel for efficient genetic stock identification of the Teno river Atlantic salmon (Salmo salar) population complex

The paper develops an SNP panel for genetic stock identification in Teno River Atlantic salmon, showing comparable performance to microsatellites with benefits in cost, speed, and robustness.