eQTL / molecular QTL mapping

The paper identifies trans-eQTLs in the human prefrontal cortex and links them to schizophrenia risk genes, showing their role in disease mechanisms.

The paper maps splice QTLs in pigs to show distinct genetic regulation of alternative splicing and overall gene expression.

The paper identifies 512 potentially causal genes for bone mineral density using TWAS and eQTL colocalization, with PPP6R3 validated in mice.

The paper introduces memento, a method for differential expression analysis of scRNA-seq data, and shows it identifies significant differences in mean, variability, and gene correlation across experimental conditions.

This study identifies ancestry-specific eQTLs in TB-T2D patients using cis-eQTL mapping, revealing variants associated with gene expression that could guide therapeutic targets in African populations.

This study identifies 135 genomic loci associated with venous thromboembolism risk through cross-ancestry GWAS and provides insights into biological pathways and potential therapeutic targets.

The paper identifies cis-QTLs and eQTLs in HS rats across five brain regions, finds colocalization with human GWAS results, and shows higher eQTL density compared to human data.

The paper identifies sex differences in schizophrenia across three brain regions using RNA-seq and genotypes, finding sex-specific genes, eQTLs, and transcriptional features.

The paper evaluates the impact of reference bias on transcriptome and eQTL analysis in mouse genetic studies and proposes improved reference strategies.

The paper identifies population-level variation in enhancer expression in the human brain and links enhancer eQTL to schizophrenia heritability.

The paper uses targeted chromatin interaction profiling to identify causal genes at type 2 diabetes GWAS loci with higher sensitivity and resolution than genome-wide methods.

The paper identifies splicing QTLs in human pancreatic islets that contribute to type 2 diabetes susceptibility by affecting gene splicing and revealing novel molecular mechanisms.

TarGene is a statistical workflow that estimates effect sizes and epistatic interactions without parametric assumptions, validated on UK Biobank data and showing genetic non-linearity and epistasis.

The paper introduces a method to identify promoter usage QTL (puQTL) using RNA-seq data, revealing novel variant-gene associations and linking them to complex traits.

This paper introduces a TBLDA framework to identify eQTLs across tissues using raw count data with a one-to-many sample-to-genotype mapping.

This paper introduces scTBLDA, a method for identifying eQTLs in single-cell RNA-seq data without relying on cell-type labels, and applies it to find cis- and trans-eQTLs in lupus patients.

This paper evaluates the use of PEER factors in single-cell eQTL analysis, showing that proper QC and transformation are needed to avoid spurious correlations and improve eQTL detection.

CellRegMap identifies context-specific regulatory variants using scRNA-seq by analyzing allelic effects across cell types and states.

This paper introduces MA-FOCUS, a multi-ancestry fine-mapping framework that improves the identification of causal genes in TWAS by leveraging ancestry-specific LD and eQTL patterns.

This paper introduces PICALO, a method to identify unknown contexts influencing eQTLs, finding 31 and 21 PICs in blood and brain datasets, respectively, associated with cell type, RNA quality, and environmental factors.

The paper identifies regulatory domains in immune cells using genomic and epigenomic data, revealing cell-type specific gene regulation and genetic control of regulatory elements.

The paper introduces FixItFelix and a modified GRCh38 reference to improve variant calling and expression analysis in genes with reference errors, showing benefits across multiple sequencing types and populations.

The paper identifies eQTL specific to NK cells and links them to autoimmunity through transcriptome-wide association studies.

The paper identifies cis- and trans-acting eQTLs influencing heat stress gene expression in maize and maps transcription factor binding footprints to prioritize functional genomic regions.

TwinEQTL provides a fast and powerful method for eQTL and GWAS analysis in twin studies by splitting twin samples and combining results with minimal power loss.

The paper quantifies RNA editing in human brain cell types, identifies cell-specific editing sites, and discovers cis-editing quantitative trait loci linked to genetic regulation.

GWAS hits (44 UK Biobank traits) and GTEx v8 cis-eQTLs (38 tissues) differ systematically: eQTLs cluster near transcription start sites of weakly constrained genes; GWAS hits favour constrained, multifunctional genes.

The paper uses drug perturbation in African American hepatocytes to identify drug response eQTLs (reQTLs) and find genetic regulators of hepatic gene expression.

This study presents the first whole genome sequences of pre-European contact Indigenous people from Uruguay, revealing connections to ancient Panama and eastern Brazil but not modern Amazonians, suggesting a distinct Atlantic coastal migration route.

This paper introduces peaBrain, a framework using convolutional neural networks to predict transcriptomic effects of non-coding variants, showing it outperforms linear models and identifies functional eQTLs.