eQTL / molecular QTL mapping

Genome-wide meta-analysis of pilonidal sinus disease and its genetic overlap with hidradenitis suppurativa, hair patterning and adiposity

This study identifies genetic risk loci for pilonidal sinus disease and finds strong genetic overlap with hidradenitis suppurativa and hair patterning, but not obesity.

Multi-omics in the All Of Us Research Program expands mapping genetic mechanisms in health and disease

The paper reports on the All of Us multi-omics cohort, identifying 182,246 QTLs and demonstrating rare variant effects across proteomic and transcriptomic data.

Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression

Single-cell eQTL mapping in 5.4 million PBMCs from 1,925 individuals with matched WGS finds common-variant eQTLs for 83% and rare-variant signals for 47% of 21,404 genes.

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

The paper shows that RNA-seq quantification methods and reference annotations significantly impact eQTL analysis, colocalization, and TWAS results across multiple tissues and phenotypes.

Genetic control and tissue specificity of transcriptomic rhythmicity

This study identifies genetic regulators of transcriptomic rhythmicity using GTEx data and links them to phenotypes in the Pan-UK Biobank.

Calibration of AlphaGenome Variant Impact and SpliceAI2 scores as PP3/BP4 evidence for missense, non-coding, and synonymous variants

The paper calibrates AlphaGenome Variant Impact (AVI) and SpliceAI2 scores for variant classification, showing their performance across different variant classes and comparison methods.

Genetic Determinants of Cell-Type-Specific Responses to Cardiotoxic Chemotherapeutic Agents

The paper identifies genetic variants associated with cardiotoxic responses to chemotherapeutic drugs using single-cell RNA-seq and eQTL analysis.

Severity-stratified, longitudinal cis-eQTL mapping enables high-sensitivity detection of candidate causal genes for critical COVID-19

This paper identifies 23 candidate causal genes for critical COVID-19 by integrating severity-stratified, longitudinal cis-eQTL mapping with GWAS signals from 1,031 patients.

Sequence-based variant-effect predictions reveal trait-specific regulatory-layer profiles of complex-trait heritability

The paper uses sequence-based variant-effect predictions to show that different regulatory layers contribute variably to the heritability of complex traits within tissues.

Genome-wide parallelism in divergence and diversity across three Hydrophis sea snake species

This study examines genomic divergence and diversity in three Hydrophis sea snake species, finding shared demographic patterns and linked selection, with chemosensory genes showing elevated diversity.

Cerberus: bidirectional state space blocks improve accuracy and efficiency of regulatory sequence models

The paper introduces Cerberus, an improved regulatory sequence model using bidirectional state space blocks, achieving higher accuracy and efficiency than existing models like Borzoi.

Strong correlations between mutation rates and selective constraint in the human genome?

The paper investigates the relationship between mutation rates and selective constraint in the human genome, finding higher mutation rates in protein-coding genes compared to non-coding regions.

Placental cis-eQTL analysis identifies preeclampsia-dependent genetic regulation at promoters

The paper identifies PE-dependent genetic regulation at promoters using cis-eQTL analysis of placental RNA sequencing data from the FINNPEC cohort.

Reconstructing donor genotypes from scRNA-seq for downstream eQTL and HLA-TCR analysis

This paper introduces scTAPAS, a method to reconstruct donor genotypes from scRNA-seq data, enabling eQTL and HLA-TCR analysis without conventional genotyping.

Significance filtering induces denominator selection bias in local genetic correlation: closed-form characterisation, a gate-aware correction, and an applicability diagnostic

The paper identifies a bias in local genetic correlation estimation due to significance filtering and proposes a correction method with a diagnostic tool.

Utilizing single-cell data for per-cell type eQTL mapping in the human pancreas

This study identifies cell type-specific eQTLs in the human pancreas using single-cell RNA-seq data and deconvoluted bulk RNA-seq data, revealing new genetic signals and associations with metabolic disease.

The Flame Retardant Triphenyl Phosphate Induces Varying Responses in Genetically Diverse Mouse Induced Pluripotent Stem Cells

The study examines how genetic variation in mouse induced pluripotent stem cells affects gene expression and cell cycle responses to triphenyl phosphate exposure.

Efficient genome-wide mapping of reproducible, context-dependent eQTLs at single-cell resolution

The paper introduces Dynema, a method for genome-wide mapping of context-dependent and independent eQTLs at single-cell resolution, showing improved detection compared to pseudobulking approaches.

PanVasc Research for AI assisted evidence analysis in panvascular intervention

The paper evaluates an AI framework for evidence analysis in panvascular intervention using clinical trial data and NLI4CT tasks, showing improved accuracy with checklist prompts over generic ones.

Maternal immune gene expression trajectories and dynamic genetic regulation throughout pregnancy

This study tracks maternal immune gene expression and genetic regulation throughout pregnancy, revealing dynamic changes and genetic interactions linked to pregnancy complications.

CDSeq2 integrates individual-level cell-type expression deconvolution with recoverability-guided prioritization

CDSeq2 improves expression deconvolution and eQTL analysis by integrating Bayesian deconvolution with prioritization of recoverable profiles in bulk RNA-seq data.

Single-cell multiomic QTL mapping reveals state-dependent genetic regulation and associated gene during cellular senescence

The paper uses single-cell multiome data to identify QTLs regulating gene expression and chromatin accessibility during cellular senescence, revealing new causal variants and regulatory mechanisms.

Distinct genetic architectures of mRNA expression and splicing QTL in the Diversity Outbred mouse population

The paper maps eQTL, isoQTL, irQTL, and sQTL in DO mice, showing distinct genetic effects on mRNA expression and splicing, and identifies candidate genes and regulatory mechanisms.

Seven replicated genomic associations of myalgic encephalomyelitis/chronic fatigue syndrome: a biobank study

Targeted-learning GWAS of 1,268 UK Biobank ME/CFS cases found 176 FDR-significant variants; seven replicated in disjoint UK Biobank or All of Us cohorts.

Scalable context-dependent single-cell eQTL mapping reveals disease-relevant regulatory variation beyond static models

The paper introduces CASTIE, a method for context-dependent eQTL mapping in single-cell data, identifying regulatory variants missed by static models and linking them to disease traits.

Multi-ancestry MHC-pQTL mapping reveals disease-linked HLA protein networks and shared genetic architecture

This study maps MHC-pQTL across ancestries, identifying genetic associations with plasma proteins and linking HLA genes to immune-related traits.

Beyond Exons: Linking Noncoding Heritability and Polygenicity across Complex Human Traits and Disorders

The paper quantifies how heritability is distributed across genomic regions for different polygenicity levels in complex traits, showing exons contribute less and intergenic regions more in highly polygenic traits.

Multiparental RNA-seq driven eQTL screening identifies loci underlying host plant fitness in a generalist herbivore

The paper identifies trans-eQTL hotspots in T. urticae linked to host plant fitness using a multiparental RNA-seq approach.

Evaluating Aggregated Gene Level eQTL Scores

The paper evaluates how different model architectures, LD filtering thresholds, and variant prioritization methods affect gene-level eQTL score prediction quality using over 3 million models.

GWAS and multimodal transcriptomic profiling of human otolithic organs characterize the genetic architecture of balance in the elderly

The paper identifies genetic factors associated with balance in the elderly through GWAS and multimodal transcriptomic analysis of otolithic organs.