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Setaria pan-genome constructed using genome assemblies of 110 representative accessions and variation analyses provides insights into foxtail millet domestication and the genetic basis for crop improvement.
A mouse model of Down syndrome (DS) highlights the importance of triplication of the IFNR gene cluster for a variety of DS-associated traits. Copy number correction resulted in amelioration of multiple phenotypes associated with the condition.
Genome-wide studies of 1,916 plasma and urine metabolites from 5,023 participants of the German Chronic Kidney Disease study provide insights into systemic and kidney-specific enzymatic and transport processes.
Genome-wide association analyses identify risk loci for spontaneous coronary artery dissection and implicate arterial integrity and tissue-mediated coagulation in the disease etiology. Several risk variants show opposite effects on coronary artery disease risk.
Analysis of rare coding variants in the UK Biobank identifies eight genes associated with adult cognitive function, including KDM5B. Rare and common variant signals overlap and contribute additively to the phenotype.
Analyses of whole-genome and RNA sequencing data from 2,733 African American, Puerto Rican and Mexican American individuals reveal ancestry-specific patterns in the genetic architecture of whole-blood gene expression.
Single-cell multiomic and functional characterization of human pancreatic islets identifies two beta cell subtypes correlated with type 2 diabetes progression that exhibit distinct gene regulatory programs and electrophysiological phenotypes.
MEGAnE is a new tool to detect and genotype mobile element variants (MEVs) from short-read whole-genome sequencing datasets. Genetic analyses implicate MEVs as population-specific drivers of gene expression variation and disease risk.
Genomic and transcriptomic analysis of 470 mostly high-risk neuroblastomas collected from 283 patients delineates subtype-specific evolutionary patterns and progression-related convergent evolution and describes the clonal dynamics of metastases.
A pan-cancer analysis of primary and metastatic tumors highlights the diversity of genetic immune escape mechanisms established during tumor evolution. The authors also present LILAC, a tool to characterize the HLA-I locus from whole-genome sequencing data.
Genome-wide association analyses across individuals of East Asian and European ancestries identify new risk loci for inflammatory bowel diseases. A polygenic risk score derived from the combined datasets shows improved prediction accuracy.
ARG-Needle is a method to infer genome-wide genealogies from large-scale genotyping data that can be used in association analyses. Applied to UK Biobank data, genealogy-based testing finds more trait associations than using imputed genotypes.
Peripheral blood mononuclear cells from 73 Japanese patients with coronavirus disease 2019 (COVID-19) and 75 healthy controls were analyzed using single-cell transcriptomics. Combining these data with genotyping data highlights the interplay between host genetics and the immune response in modulating disease severity.
Genome-wide association analyses identify 11 loci associated with native myocardial T1 time, a marker of interstitial fibrosis, providing insights into the pathways involved in myocardial fibrosis and myofibroblast cell state acquisition.
A deep convolutional neural network calculates liability scores for chronic obstructive pulmonary disease (COPD) from raw spirogram traces and noisy medical-record-based labels in the UK Biobank. Genome-wide analyses using these scores replicate known loci for lung function and identify 67 new disease loci.
‘MAximum Parsimonious Likelihood Estimation’ (MAPLE) is a maximum likelihood-based approach for inference of phylogenetic trees from very large datasets of similar sequences incorporating a sparse alignment representation and parsimony-based approximations, offering higher accuracy and reduced computational requirements.
SOX9 titration in neural crest cells identifies regulatory elements and genes with sensitive or buffered responses. Sensitive genes are enriched for craniofacial disorder genes phenocopying SOX9, suggesting differential sensitivity contributes to phenotypic specificity.
A tomato super-pangenome constructed using chromosome-scale genomes of nine wild species and two cultivated accessions highlights genomic diversity and structural variation across wild and cultivated tomatoes.
Histone H2B N-terminus multisite lysine acetylation (H2BNTac) is identified as a signature of active enhancers. H2BNTac-positive putative enhancers are validated using orthogonal enhancer activity assays.
Genomic and transcriptomic analysis of 393 non-small cell lung cancer patients treated with checkpoint inhibitors identifies molecular features associated with response.