fine-mapping

Multi-trait GWAS for diverse ancestries: Mapping the knowledge gap

This paper applies a multi-trait GWAS approach to non-European ancestries, identifying new associations and demonstrating increased replication of European loci.

Improved multi-ancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk

The paper introduces SuShiE, a model that improves multi-ancestry fine-mapping of cis-molQTLs, identifying more genes and prioritizing functionally enriched variants.

BRAIN-MAGNET: A novel functional genomics atlas coupled with convolutional neural networks facilitates clinical interpretation of disease relevant variants in non-coding regulatory elements

The paper develops BRAIN-MAGNET, a convolutional neural network that predicts non-coding regulatory element activity and helps prioritize disease-causing variants in neurogenetic disorders.

Role of Blood Lipids in the Shared Genetic Etiology Between Major Depressive Disorder and Myocardial Infarction: A Large-scale Multi-trait Association Analysis

This study identifies shared genetic risk loci and causal variants between major depressive disorder and myocardial infarction, highlighting blood lipid-related pathways and potential therapeutic targets.

Genetic determinants of plasma protein levels in the Estonian population

This study identifies genetic determinants of plasma protein levels in the Estonian population, including common, rare, and copy number variants, and provides fine-mapped credible sets for 151 proteins.

Genetic Diversity Analysis of a Multi-Gene Bank Collection of Eggplant (Solanum melongena L.): Insights from Morphological Traits and SSR Markers

The paper analyzes genetic diversity in 96 eggplant accessions using SSR markers and morphological traits to inform breeding for insect resistance.

On the contribution of genetic heterogeneity to complex traits

The paper identifies genetic heterogeneity in plants and humans using machine learning, finding allelic heterogeneity in maize eQTL and potential synthetic associations in human GWAS data.

Full epistatic interaction maps retrieve part of missing heritability and improve phenotypic prediction

This paper introduces NGG, a method that efficiently identifies epistatic interactions to explain missing heritability and improve phenotype prediction.

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

This study conducts a genome-wide association study to identify genetic variants linked to neck or shoulder pain, finding five significant loci including two novel ones and sex-specific associations.

Population structure and genetic diversity of the Critically Endangered bowmouth guitarfish (Rhina ancylostomus) in the Northwest Indian Ocean

This study assesses the genetic diversity and population structure of the bowmouth guitarfish in the Northwest Indian Ocean using mitochondrial and SNP data, revealing genetic differentiation and a cline in variation.

Pan-UK Biobank GWAS improves discovery, analysis of genetic architecture, and resolution into ancestry-enriched effects

Meta-analyzing per-ancestry GWAS of 7,266 UK Biobank traits across six genetic ancestry groups adds 14,676 loci missed by European-only analysis, including ancestry-enriched CAMK2D and G6PD signals.

Identification of new resistance QTL regions in loquat cultivar Champagne against Pseudomonas syringae pv. eriobotryae group C

This study identifies a novel QTL region on LG14 associated with resistance to loquat canker group C in the Champagne cultivar.

A novel model-free feature selection method with FDR control for omics-wide association analysis

This paper introduces a model-free feature selection method with FDR control for omics-wide association analysis, showing effective performance on simulated and real microbiome data.

Beyond guilty by association at scale: searching for causal variants on the basis of genome-wide summary statistics

This paper introduces a method to identify causal variants from genome-wide summary statistics, outperforming existing methods and discovering additional loci for complex traits.

Disentangling the shared genetics of ADHD, cannabis use disorder and cannabis use and prediction of cannabis use disorder in ADHD

This paper identifies shared genetic risk loci between ADHD, cannabis use disorder, and cannabis use, and predicts cannabis use disorder risk in ADHD using polygenic scores.

A multilayered post-GWAS analysis pipeline defines functional variants and target genes for systemic lupus erythematosus (SLE)

This paper presents a post-GWAS analysis pipeline to identify functional variants and target genes for SLE using integrative genomic and epigenomic data.

Overcoming the "feast or famine" effect: improved interaction testing in genome-wide association studies

This paper identifies a 'feast or famine' effect in genome-wide interaction studies that causes inconsistent type 1 error rates and proposes TINGA to correct for it, improving power and reliability.

An expression-directed linear mixed model (edLMM) discovering low-effect genetic variants

This paper introduces edLMM, a method that detects low-effect genetic variants using moderate sample sizes, improving missing heritability estimation.

Estimation of inbreeding and kinship coefficients via latent identity-by-descent states

This paper introduces Kindred, a method for estimating inbreeding and kinship coefficients by modeling latent identity-by-descent states, showing high accuracy and non-negativity in kinship estimates.

Integration of Expression QTLs with fine mapping via SuSiE

The paper introduces SuSiE2, a method that integrates eQTL information with fine mapping to improve causal variant identification in GWAS by leveraging expression data.

Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle

The paper identifies 41k regulatory loci in cattle reproductive tissues linked to male fertility by analyzing gene expression and splicing variation across testis, epididymis, and vas deferens.

GWAS of ~30,000 samples with bone mineral density at multiple skeletal sites and its clinical relevance on fracture prediction, genetic correlations and prioritization of drug targets

This study performs GWAS on BMD traits and fracture risk using 30,000 UK Biobank samples, identifies novel loci, and prioritizes drug targets for osteoporosis prevention.

Deep learning predicts DNA methylation regulatory variants in specific brain cell types and enhances fine mapping for brain disorders

This paper introduces a transformer-based model to predict cell type-specific DNA methylation regulatory variants and improves fine mapping for brain disorders.

Northeast India: Genetic Inconsistency across Ethnicity and Geography

The paper analyzes the genetic structure of Northeast India, finding a complex interplay between language, ethnicity, and geography, with a novel Trans-Himalayan ancestry uniting the region.

Proteo-genomics of soluble TREM2 in cerebrospinal fluid provides novel insights and identifies novel modulators for Alzheimer disease

This study identifies four novel genetic loci associated with soluble TREM2 levels in CSF through GWAS and provides functional validation of their roles in Alzheimer's disease.

A novel Bayesian fine-mapping model using a continuous global-local shrinkage prior with applications in prostate cancer analysis

This paper introduces a Bayesian fine-mapping model, h2-D2, which outperforms existing methods in identifying causal variants and applies it to prostate cancer, discovering new variants and associated genes and pathways.

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

Korea4K presents whole-genome sequences of 4,157 Koreans with 107 health parameters, identifying new genotype-phenotype associations and improving imputation performance.

SparsePro: an efficient fine-mapping method integrating summary statistics and functional annotations

SparsePro improves fine-mapping of GWAS results by integrating summary statistics and functional annotations, achieving higher power and faster computation than existing methods.

Population genomic analysis reveals high inbreeding in a Hawksbill turtle population nesting in Singapore

The paper presents a population genomic analysis of hawksbill turtles in Singapore, revealing high inbreeding and demographic impacts from past climate change.

Common genetic variation impacts molecular stress response in the brain

The paper identifies stress-interactive eQTLs that dysregulate gene expression in the brain under stress, uncovering novel genes linked to brain disorder risk in traumatic stress contexts.