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By integrating single-cell and bulk transcriptomic analyses, we found that malignant cells belong to two major intrinsic epithelial subtypes. We propose a refined, three-tiered classification of colorectal cancer subtypes based on intrinsic epithelial subtypes, microsatellite instability status and the presence of fibrosis.

A large-scale collaborative effort now provides a comprehensive annotation of functional non-coding elements in the zebrafish genome. This work serves as an essential foundation for future studies to understand how gene regulatory circuits control embryonic development.

The DANIO-CODE consortium leverages a large-scale multiomic dataset to improve zebrafish genome annotation. They identify ~140,000 cis-regulatory elements throughout development and perform a comparison with the mouse regulatory landscape.

A single-cell transcriptomic analysis of 63 patients with colorectal cancer classifies tumor cells into two epithelial subtypes. An improved tumor classification based on epithelial subtype, microsatellite stability and fibrosis reveals differences in pathway activation and metastasis.

The largest GWAS for kidney function so far provided the starting point for integrated multi-stage annotation of genetic loci. Whole kidney and single-cell epigenomic information is crucial for translating GWAS information to the identification of causal genes and pathogenetic (and potentially targetable) cellular and molecular mechanisms of kidney disease.

The use of association studies to identify candidate genes for complex biological traits in plants has been challenging due to a reliance on single reference genomes, leading to missing heritability. Graphical pangenomes and the identification of causal variants help overcome this and provide an important advance for crop breeding.

Single-cell ATAC-seq and RNA-seq profiling traces the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC). A large proportion of polyp and CRC cells show a stem-like phenotype.

Genome-wide analyses identify hundreds of loci associated with kidney function. Integrated analyses of expression, methylation and single-cell open chromatin and expression data derived from human kidney samples prioritize genes and mechanisms underlying renal disease.

Allelic imbalance analysis applied to ATAC-Seq data from 23 cancer types identifies 7,262 allele-specific accessibility quantitative trait loci, which are enriched for cancer risk heritability and altered transcription factor binding motifs.

Genome-wide analyses of cardiovascular magnetic resonance images identify variants associated with right ventricular structure and function. Polygenic scores for these traits are associated with dilated cardiomyopathy and coronary artery disease.

Genome-wide analyses of cardiac magnetic resonance imaging data identify loci associated with right heart structure and function. A polygenic predictor of right ventricular ejection fraction is associated with dilated cardiomyopathy risk.

Recent work has highlighted a lack of diversity in genomic studies. However, less attention has been given to epigenomics. Here, we show that epigenomic studies are lacking in diversity and propose several solutions to address this problem.

A genomic analysis of ductal carcinoma in situ (DCIS) samples with matched ipsilateral invasive breast cancer recurring later shows that around 18% of tumors were unrelated to the DCIS, and had distinct clonal origins.

snipar is a software package for imputing missing parental genotypes and estimating direct genetic effects. Application to UK Biobank data shows that effects estimated by standard genome-wide association study designs have confounding bias for some phenotypes.

SMARCE1 loss destabilizes the canonical BAF complex and increases the formation of BRD9-containing non-canonical (ncBAF) complexes. SMARCE1-deficient cells, which are a model for clear cell meningioma, are sensitive to ncBAF complex inhibition.