eQTL / molecular QTL mapping

The paper identifies human-specific methylated regions enriched in schizophrenia GWAS signals and shows their enrichment surpasses other evolutionary markers.

This study conducts a GWAS on depression phenotypes in UK Biobank, identifying genetic variants enriched in excitatory synaptic pathways.

This study performs a large GWAS of Alzheimer's disease, identifies four new risk loci, and highlights pathways involving immunity, lipid metabolism, and APP/Aβ processing.

The paper challenges the validity of S-LDSC by showing it produces unreliable enrichment estimates and defends the LDAK Model as more accurate for SNP heritability analysis.

This paper introduces a Bayesian framework to identify regulatory effects at GWAS risk loci by integrating GWAS summary data with molecular QTL data.

The paper integrates chromatin accessibility and DNA methylation data from human pancreatic islets to refine regulatory mechanisms at Type 2 Diabetes susceptibility loci.

The paper identifies haplotypes and LD patterns in 80 genes that differ between breast cancer patients and controls, and finds negative correlations in LD patterns for some genes.

This paper develops a statistical method that uses allele-specific expression and eQTL data to improve fine-mapping of causal variants for gene expression, achieving higher specificity than eQTL-only approaches.

The paper introduces a new relation measure, Linkage Probability, to analyze genetic data and reveals 3D chromatin loop effects in SNP data.

The paper decomposes transcriptional activity to identify how much is influenced by chromatin architecture and cell-specific regulatory interactions across 76 human cell types.

This study maps cis-regulatory variation in budding yeast with high-resolution eQTLs, revealing roles of non-promoter variants and selection pressures on gene expression.

The paper examines DNA hypermethylation in developmental contexts, identifying gene-specific methylation patterns and their links to transcriptional regulation in human cell types.

The paper generates a transcriptome resource and eQTL catalogue in vervet monkeys, revealing sex and age-related expression patterns and key regulatory loci.

This paper estimates the causal tissues for complex traits and diseases by analyzing eQTLs from the GTEx consortium and adapting the RTC score to calculate tissue sharing probabilities.

The paper uses whole genome sequence and RNA-seq to predict causal variants affecting gene expression and identifies high confidence causal variants enriched in GWAS associations.

This paper shows that analyzing RNA-Seq data at multiple resolutions increases the detection of causal eQTLs in autoimmune diseases, revealing more loci with shared genetic effects than gene-level analysis alone.

This paper introduces a statistical method to map eQTLs by integrating genetic, epigenetic, and tissue-specific factors, improving detection power over existing approaches.

This paper introduces log allelic fold change (aFC) as a measure for quantifying cis-eQTL effect sizes, showing its consistency across datasets and independence from expression level and allele frequency.

The paper identifies ACVR1B as a candidate causal gene for emphysema distribution by integrating GWAS, eQTL, and epigenomic data.

JEPEGMIX2 improves gene-level eQTL analysis by using updated cis-eQTL SNPs and adjusting for background enrichment, reducing false positives in cosmopolitan cohorts.

FUN-LDA predicts tissue-specific functional effects of noncoding variants by integrating epigenetic data, showing higher accuracy than existing methods in eQTL and GWAS analyses.

The paper investigates the genetic regulation of 63 lipid metabolism genes in pig skeletal muscle using eQTL analysis and identifies 12 cis- and 18 trans-eQTLs affecting 19 loci.

This study identifies genes affecting social reinstatement behavior in chickens using QTL and eQTL analysis, finding TTRAP as a strong candidate gene and suggesting clustered genetic modules drive domestication.

This paper compares different prior distributions and genomic window strategies for genome-wide association analysis, finding that heavy-tailed and variable selection priors with adaptive windows perform best.

The paper evaluates chromatin accessibility in prefrontal cortex samples from schizophrenia cases and controls, finding high heritability enrichment in open chromatin regions but no differential accessibility between groups.

QTLtools is a modular framework for molecular QTL discovery and analysis, integrating data preparation, molQTL detection, and GWAS variant integration.

The paper develops a method to infer allelic heterogeneity in GWAS and eQTL datasets, identifying 4152 loci with strong evidence of AH across different traits.

The paper shows that population size affects the ratio of AT→GC to GC→AT variants, with larger populations having higher ratios due to GC-biased gene conversion.

The paper introduces a meta-analysis method to identify eQTLs from multi-tissue datasets, detecting more eQTLs and eGenes than previous approaches.

The paper identifies trans-eQTLs that affect multiple transcripts and mediate transcriptional co-regulation across populations.