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In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

De novo and inherited dominant variants in genes encoding U4 and U6 small nuclear RNAs are identified in individuals with retinitis pigmentosa. The variants cluster at nucleotide positions distinct from those implicated in neurodevelopmental disorders.

Negative regulation of the cGAS-STING pathway is crucial to limit damaging inflammation. Here, by combining in vitro experiments and myeloid cell-specific conditional knockout mice, the authors identify the autophagy receptor TAX1BP1 as a negative regulator of STING by targeting it for degradation through Golgiphagy and ESCRT-mediated microautophagy.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

Interface engineering is promising for advancing perovskite solar cell (PSC) performance and longevity. This Review highlights three emerging strategies for interfacial optimization in PSCs: multifunctional molecular passivation, heterostructures and self-assembled monolayers. The authors discuss relevant materials, assess their limitations and outline challenges and prospective directions for future research.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

Systematic analysis from the Global Burden of Disease study reported that, despite global improvements from 1990 to 2021, dietary iron deficiency-associated disease burden remains high in women, children and residents in low socio-demographic index countries.

Fourteen months after treatment with engineered immune cells, the recipient has no symptoms and doesn’t need to take medication.

Whole-genome sequencing, transcriptome-wide association and fine-mapping analyses in over 7,000 individuals with critical COVID-19 are used to identify 16 independent variants that are associated with severe illness in COVID-19.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

Climate patterns in the Pacific Ocean, such as El Niño, are known to significantly affect marine life. This study suggests that, contrary to expectations, El Niño can actually increase ocean biomass in the western tropical Pacific, a finding that is crucial for improving predictions of how fisheries may respond to future climate change.

A multimodal deep learning model combines molecular sequence, structure and biochemical properties to predict immunogenicity in an interpretable way, providing a framework for smarter molecular prediction and hypothesis generation.

In a randomized controlled study involving 58 physicians in Pakistan, assistance by a large language model in diagnostic reasoning resulted in a 27.5% increase in performance on 6 clinical vignettes.

While desirable for compact solutions, the miniaturization of spectrometers comes at the cost of spectral resolution and operating range. Here, Wanet al. propose a tapered fibre multimode interference spectrometer exhibiting high spectral resolution from the visible to the near infrared in a compact configuration.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

Mitochondria are key to powering the immune defenders called dendritic cells.

A meta-analysis of genome-wide association studies of type 2 diabetes (T2D) identifies more than 600 T2D-associated loci; integrating physiological trait and single-cell chromatin accessibility data at these loci sheds light on heterogeneity within the T2D phenotype.

A mass spectrometry-based approach globally identifies protein regulators of metabolism and reveals the role of LRRC58 in controlling cysteine catabolism.

GIANT, a genetically informed brain atlas, integrates genetic heritability with neuroanatomy. It shows strong neuroanatomical validity and surpasses traditional atlases in discovery power for brain imaging genomics.

Activin receptor-like kinase 4 (ALK4) is frequently downregulated or mutated in cancers. Here the authors find that ALK4 loss promotes canonical TGF-β signaling and cancer progression through increasing TGF-β receptor N-linked glycosylation and subsequently stabilizing these receptors at the cell surface.

Metal halide perovskites have been studied as promising materials for blue light-emitting diodes (LEDs) but the stability is still a bottleneck. Here Wang et al. develop a chelating additive strategy to increase efficiency, operational stability and color stability of blue perovskite LEDs.

The production of higher alcohols is very valuable because of their high volumetric energy density. Now, Sargent, Sinton and co-workers report the design of copper nanoparticles with tailored nanocavities that promote n-propanol formation by the coupling of C2 and C1 intermediates inside the cavity.

The authors identify 92 tick-associated viruses, including ten pathogenic to humans in northwest China and adjacent countries. They predict a significant increase of major pathogenic viruses and their vectors in high-risk regions.

Tumor suppressor PALB2 is known to interact with BRCA1 and BRCA2, and to be required for the latter's localization to sites of DNA damage. Now PALB2 is shown to bind directly to DNA, to recombinase RAD51 and its accessory factor RAD51AP1. PALB2 also stimulates D loop formation by RAD51 in a synergistic manner with RAD51AP1.

The electro-oxidative synthesis of valued chemicals offers to enhance the overall efficiency and economic viability of renewable electrosynthesis systems. Here, the authors use dopant-tuned catalysts to promote the electrosynthesis of dimethyl carbonate from CO and methanol via oxidative carbonylation.

Machine learning predicts Cu-Al electrocatalysts provide better efficiency and productivity than copper when using intermittent renewable electricity to convert carbon dioxide to useful chemicals and fuels.

CellSAM uses an object detector, CellFinder, to detect cells and prompt the Segment Anything Model (SAM) to generate segmentations. This universal model achieves human-level performance across a range of bioimaging data encompassing mammalian cells, yeast and bacteria.

A study of several longitudinal birth cohorts and cross-sectional cohorts finds only moderate overlap in genetic variants between autism that is diagnosed earlier and that diagnosed later, so they may represent aetiologically different conditions.

He and colleagues develop LucaOne, a biological foundation model pre-trained on nucleic acid and protein sequences from 169,861 species. It shows an emerging understanding of molecular biology’s central dogma, enhancing bioinformatics analysis and helping explore unknown aspects of molecular biology.