Classes of autism are uncovered with a generative mixture modeling approach leveraging matched phenotypic and genetic data from a large cohort, revealing different genetic programs underlying their phenotypic and clinical traits.

Here the authors show that chromosomal instability signatures can predict resistance to anthracycline-, taxane- and platinum-based chemotherapeutics in breast, ovarian and prostate cancer and sarcoma. Validation is performed through emulation of phase 2 and 3 clinical trials using real-world data.

A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for epithelial colonization.

scMicro-C is a new method that provides high-resolution maps of the 3D genome. scMicro-C identifies structures called ‘promoter stripes’, which link a gene promoter to multiple downstream enhancers.

A genome-wide association study in rice identifies variation in SBRR1 associated with sheath blight resistance. Introducing the SBRR1-R allele into a commercial rice variety reduces yield loss under severe exposure to sheath blight disease.

De novo long-read genome assembly for nine legume species and pangenome analysis identify genomic variations associated with environmental adaptation and domestication and highlight the role of transposable elements in genome evolution.

Genome-wide analyses in over one million self-reported cases and controls identify genetic variants associated with stuttering and find genetic correlations with autism, depression and impaired musical rhythm, supporting a potential neurological basis for stuttering.

ESCAPE-seq (enhanced single-chain antigen presentation sequencing) is a massively parallel platform for screening of class I HLA–peptide combinations for antigen presentation. The authors assess more than 75,000 peptide–HLA combinations, revealing presented epitopes from oncogenic driver mutations and fusions across diverse HLA-A, HLA-B and HLA-C alleles.

A single-cell multiomic immune cell atlas from 235 Japanese, including patients with COVID-19 and healthy individuals, linked with host genetics including germline and somatic mutation, plasma proteomics and metagenomics data reveals that immune cells are dynamically regulated in a cell state-dependent manner.

Genome assemblies of two allotetraploid cotton germplasms, Jin668 and YZ1, reveal the regulatory mechanisms underlying somatic embryogenesis and plant regeneration, and provide potential for precise genome editing in cotton.