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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.
A new study employs CRISPR–Cas9-based base editing for simultaneous mutagenesis of all copies of histone H3 genes in mammals, highlighting the functional importance of H3K27me3 for Polycomb-mediated gene silencing and the dispensability of H3K27ac in transcriptional activation.
A new study highlights a strategy to link SNPs implicated in human complex traits and diseases with probable causal genes. This method prioritizes genes for functional characterization and helps address questions about the architecture of human phenotypes.
Calls for diversity in genomics have motivated new global research collaborations across institutions with highly imbalanced resources. We describe practical lessons we have learned so far from designing multidisciplinary international research and capacity-building programs that prioritize equity in two intertwined programs — the NeuroGAP-Psychosis research study and GINGER training program — spanning institutions in Ethiopia, Kenya, South Africa, Uganda and the United States.
CRISPR editing of all 28 alleles encoding histones H3.1, H3.2 and H3.3 in mouse embryonic stem cells (mESCs) generates pan-H3K27R mutant mESCs, which are transcriptionally similar to PRC2-null mESCs. H3K27 acetylation is dispensable for gene derepression in mESCs and for gene activation in epiblast-like cells.
