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The study reports the arrival of avian influenza H5N1 virus clade 2.3.4.4b into the Indian Ocean sub-Antarctic archipelagos of Crozet and Kerguelen. Using phylogeographic analyses, the virus likely came from the distant South Georgia islands.

Integrated multi-omic analyses using samples from the TRACERx study highlight cross-talk between DNA hypermethylation and genomic lesions in non-small cell lung cancer.

Warming ocean water plays a significant role in accelerating Arctic sea ice melt. Here the authors present detailed observations of warm water of Pacific origin entering and diving beneath the Arctic ocean surface, and explore the dynamical processes governing its evolution.

Here the authors show that loss of TANGO2, a gene linked to an autosomal recessive disorder characterised by developmental delay, rhabdomyolysis, cardiac arrhythmias and metabolic disturbances, disrupts mitochondrial and cytoskeletal structure by impairing its interaction with CRYAB, leading to desmin aggregation and desminopathy, causing cardiomyopathy, muscle weakness, and metabolic dysfunction in mice and human cells.

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).

The conversion of solar energy into electricity usually occurs either electrically or through thermal conversion. A new mechanism, photon-enhanced thermionic emission, which combines electric as well as thermal conversion mechanisms, is now shown to lead to enhanced conversion efficiencies that potentially could even exceed the theoretical limits of conventional photovoltaic cells.

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.

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.

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.

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.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

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.

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.

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.

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.

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.

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.

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 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.

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.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

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.

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.

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.

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.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Lee et al. use three-dimensional cell reconstruction of focused ion beam scanning electron microscopy data and multi-omics to show that ether-lipid metabolism regulates inter-organelle biogenesis and dynamics.

Openshaw and colleagues find myeloid inflammation and complement activation signatures in patients with long COVID who were previously hospitalized.

Transcriptome-wide association studies (TWAS) have identified colorectal cancer (CRC) susceptibility genes. Here, the authors combine two multi-tissue TWAS methods, Mendelian randomisation, and genetic colocalization to identify 37 likely causal CRC susceptibility genes.

Upon stimulation of receptors, NAADP is formed as calcium-mobilizing second messenger in many cells. Here, the authors develop MASTER-NAADP, a membrane-permeant precursor of NAADP, and characterize its biological activity.

Current imaging flow cytometry approaches remain limited in their ability to reveal subcellular information with high-resolution and instrumental simplicity. Here, the authors present a light-field flow cytometer capable of high-content, multi-color imaging of cells with high-resolution in 3D.

Methods for imaging the 3D cell surface often require physical interaction. Here the authors report the combination of scanning ion conductance microscopy (SICM) and live-cell super-resolution optical fluctuation imaging (SOFI) for the non-invasive topographical imaging of soft biological samples.

How the necroptosis executioner, MLKL, converts to a killer form has been mysterious. Here, authors show RIPK3-mediated phosphorylation of human MLKL is the cue for pseudokinase domain dimerization before assembly of pro-necroptotic MLKL tetramers.

Paul Pharoah and colleagues report the results of a large genome-wide association study of ovarian cancer. They identify new susceptibility loci for different epithelial ovarian cancer histotypes and use integrated analyses of genes and regulatory features at each locus to predict candidate susceptibility genes, including OBFC1.

Recent crystal structures of DNA polymerases provide new insights into conformational dynamics and DNA minor groove interactions that are critical for efficient and accurate DNA synthesis.

This paper proposes a framework to assess systemic risks that compound and cascade within and between systems. This emphasizes political economy and transformations, as well as trans-disciplinarity and diverse participation, evidence and methods.

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.

Integrating tunable quantum emitters with commercial photonic circuits is promising for quantum information applications but remains a challenge. Here the authors report integration of InAs/InP microchiplets containing quantum dot single photon emitters into a large-scale foundry silicon platform.

A legal case about public access to documents is raising questions about the US Department of Energy's scrutiny of alleged scientific misconduct.

Immune lymphocyte estimation from nucleotide sequencing (ImmuneLENS) infers B cell and T cell fractions from whole-genome sequencing data. Applied to the 100,000 Genomes Project datasets, circulating T cell fraction provides sex-dependent and prognostic insights in patients.

The NUP98–HOXA9 oncogenic fusion protein found in leukaemia undergoes phase separation in the nucleus, which helps to promote activation of leukaemic genes and to establish aberrant chromatin looping.

Dimethyl fumarate (DMF) is an anti-inflammatory drug proposed as a treatment for COVID19. Here the results are reported from a randomised trial testing DMF treatment in 713 patients hospitalised with COVID-19. DMF was not associated with any improvement in day 5 outcomes.

Photoluminescence microscopy can give information on the electronic properties of optoelectronic materials and thus the performance of optoelectronic devices. In this Primer, Wei et al. cover experimental set-ups for photoluminescence microscopy, including widefield and confocal configurations, and considerations for data acquisition and analysis.