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GeNA identifies cell-state abundance quantitative trait loci (csaQTLs) in single-cell RNA sequencing data. Applied to OneK1K, GeNA identifies natural killer cell and myeloid csaQTLs and implicates interferon-α-related cell states using a polygenic risk score for systemic lupus erythematosus.
Comparison of association signals in UK Biobank using different strategies for assessing genetic variation shows that whole-exome sequencing combined with array genotyping and imputation offers similar performance to whole-genome sequencing at a reduced cost.
Deep rare variant association testing (DeepRVAT) is a deep set neural network model that flexibly integrates rare variant annotations into a trait-agnostic gene impairment score. These scores improve association testing and polygenic risk prediction.
Statistical fine-mapping of mRNA and protein quantitative trait loci in blood samples from the Japan COVID-19 Task Force sheds light on regulatory mechanisms and disease associations.
Phylogenetic analysis of trait heritability (PATH) applies phylogenetic correlations to single-cell lineage tracing data, quantifying cell state plasticity and transition probabilities. PATH offers insights into cell state heritability and transition dynamics in cancers.
Phenome-wide analysis in the UK Biobank identifies GC-rich tandem repeat expansions associated with a range of traits, including a GCC expansion in AFF3 contributing to intellectual disability.
Epithelioids are genetically stable, self-sustaining three-dimensional cultures. They may be used to investigate various aspects of epithelial biology over several months without need for passaging. In this paper, mouse epithelioids are used to identify drivers of clonal expansion in the esophagus.
Analysis of autosomal recessive coding variants in 29,745 trios from the DDD study and GeneDx provides insights into the genetic architecture of developmental disorders across ancestrally diverse populations.
A large-scale multi-ancestry genome-wide association study of European, African, admixed American, South Asian and East Asian ancestries provides insights into the pathogenesis of anxiety disorders.
Chemically driven blockade of PU.1 binding sites leads to its genome-wide redistribution. PU.1 network rewiring causes human acute myeloid leukemia cells to differentiate.
Spot-based spatial transcriptomic analysis of paired primary and metastatic pancreatic cancers identifies cellular, metabolic and fibrotic changes in ecotypes associated with progression, highlighting the contribution of the tumor microenvironment.
CREME is an extensible computational tool for investigating cis-regulation via in silico perturbations of neural network-based DNA sequence models such as Enformer, identifying complex interactions between a gene’s regulatory elements.
Single-cell profiling of lamina-associated domains (LADs) during early mouse development reveals an overlap between preimplantation-specific LAD dissociation and noncanonical broad H3K27me3 domains. Loss of H3K27me3 restores canonical LAD profiles.
Analysis of human tumor datasets shows that all features that appear significantly associated with immunotherapy response and survival may be collapsed into five latent factors: tumor mutation burden, T cell effective infiltration, TGF-β activity in the microenvironment, prior treatment and tumor proliferative potential.
Massively parallel reporter assays in four plant species show that transcriptional regulatory elements are position dependent with enrichment downstream of the transcription start site, particularly GATC motifs with strong effects in vascular plants.
MILTON uses phenotype information in the UK Biobank to identify clinical biomarkers and other quantitative traits that characterize diseases. It then constructs augmented cohorts by predicting undiagnosed individuals, improving power to discover gene–disease relationships.
Microfluidics-assisted grid chips for spatial transcriptome sequencing (MAGIC-seq) is a spatial transcriptomics method combining multiple-grid microfluidic design and prefabricated DNA arrays for increased throughput and reduced cost, with applications for large fields of view and 3D spatial mapping.
Hi-C analysis identifies Xist-separated megadomains (X-megadomains) on the inactive X chromosome in mouse early embryos. Cohesin loading at Xist regulatory elements promotes X-megadomain formation and restricts nearby gene activity.
Integration of genome-wide association analysis of 406,504 individuals in the UK Biobank and scATAC–seq data reveals that variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function.