Research articles

Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence conservation.

Base editing of the pathogenic trinucleotide repeat expansions underlying Huntington’s disease and Friedreich’s ataxia introduces repeat interruptions that reduce somatic expansion in patient cells and mice.

A genome-wide study by the Long COVID Host Genetics Initiative identifies an association between the FOXP4 locus and long COVID, implicating altered lung function in its pathophysiology.

The genomic features of precursor conditions of multiple myeloma provide multiple biological insights into disease origins and evolution, together with opportunities to identify those at highest risk of progression.

Disequilibrium genome-based restricted maximum likelihood (DGREML) simultaneously quantifies the contribution of SNPs and their directional covariances to trait heritability and shows that cross-autosomal correlations contribute substantially to SNP-based heritability for many complex traits.

Analysis of a large cohort of metastatic breast cancer samples shows that APOBEC mutational signatures are enriched in post-treatment samples. APOBEC activity was also associated with mutations known to drive drug resistance.

Analysis of snRNA genes in individuals with rare disorders identifies de novo and recurrent variants in RNU5B-1 and RNU5A-1, in addition to previously unreported cases with pathogenic or likely pathogenic variants in RNU4-2.

Genome-wide analyses identify 30 independent loci associated with obsessive–compulsive disorder, highlighting genetic overlap with other psychiatric disorders and implicating putative effector genes and cell types contributing to its etiology.

The human endoderm-derived organoid cell atlas (HEOCA) presents an integrative analysis of single-cell transcriptomes across different conditions, sources and protocols. It compares cell types and states between models, and harmonizes cell annotations through mapping to primary tissues.

This study characterizes the three-dimensional (3D) genome architecture of 15 primary human cancer types from The Cancer Genome Atlas. The analyses identify different archetypes of enhancer usage and enhancer rewiring events due to different classes of mutations and structural variants.

Comparison of paired primary and recurrent glioblastomas at the single-cell transcriptomic level describes molecular and cellular trajectories associated with tumor recurrence, highlighting extensive heterogeneity and microenvironmental co-evolution.

Integrated single-cell transcriptomic and genetic characterization of 121 adult glioblastomas identifies heterogeneity at cell type, cell state and baseline expression program levels associated with specific mutations that form three stereotypical ecosystems.

Generation and analysis of high-quality, genome assemblies from Middle Eastern trios demonstrate the utility of ancestry-matched data and assembly-based variation analysis.

A graph-based peanut pangenome constructed using 6 newly assembled and 2 previously published genomes and 269 resequenced accessions highlights the contribution of structural variants to pod size.

Chromosome-level genome assemblies of nine tetraploid and two diploid wild Oryza species provide insights into genome evolution within the genus Oryza and the potential for crop improvement and neodomestication.

Pan-genome analysis of 24 alfalfa accessions identifies key structural variations associated with salt tolerance and quality traits and provides resources for genomics-assisted breeding in alfalfa.

Multi-omic analysis of the developing mouse kidney shows strong sex-dependent differences in gene expression during development and aging. These differences are likely mediated by sex hormones.

Transcriptome-wide analysis of differential expression (TRADE) is a broadly applicable tool for characterizing patterns of differential expression across the genome.

In cutaneous melanoma, desmosome genes are frequently affected by coding mutations that decrease their expression. This decrease in expression occurs predominantly in keratinocytes in the tumor microenvironment and can induce hyperproliferation of adjacent melanoma cells in coculture.

A graph-based pan-genome constructed from 30 genome assemblies covering Malus domestica ‘Golden Delicious’ and 29 wild diploid or polyploid Malus species highlights structural variation and genome evolution in the Malus genus.