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This study examines karyotypic selection and evolution in vitro using immortalized mammary and kidney epithelial cell lines, observing aneuploidy patterns specific to each origin tissue that are correlated with frequencies in patient tumors and independent of drivers such as TP53 mutation.
Resequencing of 390 peanut accessions provides insights into peanut migration and diversity in China. Genome-wide association analysis identifies loci associated with 28 agronomic traits.
Lentiviral massively parallel reporter assay (lentiMPRA) analysis of cardiac cis-regulatory elements characterizes the effects of noncoding de novo variants identified in congenital heart disease. EpiCard is a model for variant prioritization.
We constructed a pan-genome using 27 high-quality representative Brassica oleracea genomes. Using this pan-genome, together with multi-omics datasets from large-scale populations, we uncovered the important role of structural variations as dosage regulators of gene expression, which drives the morphotype diversification in B. oleracea.
Multi-omic analysis of 100 clear cell renal cell carcinomas identifies four transcriptomic subgroups (IM1–IM4). IM4 is a high-risk subtype characterized by specific metabolic changes and a loss of lipid droplets.
A genome-wide CRISPR knockout screen in eHAP cells using ATAC-see to fluorescently label chromatin identifies novel regulators of accessibility, such as the transcription factor TFDP1 via regulation of canonical histone expression.
MuSiCal is a mutational signature analysis tool combining minimum-volume nonnegative matrix factorization with other algorithmic innovations. Applied to PCAWG data, MuSiCal gives more accurate results, including resolving ambiguous flat signatures.
In vivo tracing of the single-cell 3D structure at the Hoxa cluster shows that Polycomb-associated domains in individual cells are flexible and often decompact while maintaining a repressive transcriptional state.
A common architectural feature of the genome in many organisms is chromatin domains. A synthetic biology approach now builds chromatin domains from scratch and identifies some of the minimal components needed for their formation.
Analysis of colorectal cancer bulk gene expression data at the pathway level identifies a poor-prognosis subtype associated with cell differentiation. The subtypes are reproducible in single-cell data and offer biological insights beyond existing stratification strategies.
De novo genome assemblies of 22 Brassica oleracea accessions and pan-genome analyses highlight the effects of structural variations on gene expression and their contributions to morphotype diversification.
Near-gapless and haplotype-resolved genome assemblies of the dwarfing ‘M9’ and semi-vigorous ‘MM106’ rootstocks and a major apple cultivar ‘Fuji’ provide insights into the genetic basis of rootstock-induced dwarfing traits.
An open-source automated algorithm called DeepFlow enables large-scale derivation of aortic flow measurements, and genetic analysis of aortic flow, structural and functional traits demonstrates a causal relationship between aortic size and aortic valve regurgitation.
Achieving a diagnosis for Indigenous people living with a rare, often genetic, disease is crucial for equitable healthcare. The International Rare Disease Research Consortium convened a global Task Force to bridge the gap in diagnosing Indigenous rare diseases, and identify solutions to tackle the health inequity faced by Indigenous people.
Understanding clinical heterogeneity in attention deficit hyperactivity disorder (ADHD) is important for improving personalized care and long-term outcomes. A study exploits the large scale and breadth of phenotyping of the iPSYCH cohort to link clinical heterogeneity to genetic heterogeneity in ADHD.
Fluorescence-activated nuclear sorting combined with deep profiling shows that Huntington’s disease repeat expansions arise in specific cell types and are associated with elevated MSH2 and MSH3, which promote expansions in vitro by inhibiting excision of CAG slip-outs by FAN1.