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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.
Disruption of MLL3/4 enzymatic activities prevents gastrulation and leads to early embryonic lethality in mice. This is largely due to defects in extraembryonic lineages, which compromise developmental progression.
Single-cell analysis of head and neck squamous cell carcinoma (HNSCC), specifically from human papillomavirus (HPV)-positive and HPV-negative oropharynx tumors, reveals high levels of inter- and intratumoral heterogeneity. Patterns of HPV gene expression were divergent within HPV-positive tumors, with corresponding functional effects on treatment resistance.
High-resolution Micro-C is applied to characterize the effect of RNA polymerase II (RNAPII) loss on chromosome looping, finding that the formation of enhancer–promoter, but not promoter–promoter, loops are dependent on RNAPII binding to their anchors.
Analysis of multiple tumor types, cancer cell lines and adult tissues identifies tumor-specific transposable-element-chimeric transcripts. Mass spectrometry data confirm that many are translated and subsequently located on the extracellular surface of cancer cells, highlighting potential immunogenic therapies.
Somatic evolutionary analysis of neuroblastoma, a pediatric tumor, proposes a common fetal time of origin. Notably, high-risk tumors exhibit early genomic instability and prolonged evolution, and this evolutionary duration predicts clinical outcomes.
Genome-wide CRISPR screening identifies thymidine nucleotide metabolism as a key regulator of human telomere length. Thymidine supplementation promotes telomere elongation in cells derived from patients with telomere biology disorders.