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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.

Western Amazon rivers play a critical and underrecognized role in sustaining the Amazon Basin’s ecological integrity, according to analysis of the status of the hydrology and sediments, biodiversity, and longitudinal connectivity across the region.

Natural ecosystems efficiently sequester CO₂, but containing and controlling living systems remains challenging. Here, the authors engineer a photosynthetic living material for dual CO₂ sequestration via biomass accumulation and microbially-induced calcium carbonate precipitation.

Analysing camera-trap data of 163 mammal species before and after the onset of COVID-19 lockdowns, the authors show that responses to human activity are dependent on the degree to which the landscape is modified by humans, with carnivores being especially sensitive.

Analysis of HbA1c and FPG levels across 117 population-based studies demonstrates regional variation in prevalence of previously undiagnosed screen-detected diabetes using one or both measures and suggests that use of elevated FPG alone could underestimate diabetes prevalence in low- and middle-income countries.

Genotype and exome sequencing of 150,000 participants and whole-genome sequencing of 9,950 selected individuals recruited into the Mexico City Prospective Study constitute a valuable, publicly available resource of non-European sequencing data.

Tailored to provide diabetes management recommendations from large training and validation datasets, an artificial intelligence system integrating language and computer vision capabilities is shown to improve self-management of patients in a prospective implementation study.

The economy and banks in the euro area contribute and are exposed to nature-related risks, according to an analysis of data on 2500 banks’ dependence and impact on biodiversity, ecosystem degradation, and climate change.

Given the scarcity and cost of platinum, it is important to develop sustainable processes for its recycling. Here, the authors report the dissolution of metallic platinum using reductive and oxidative gases to repetitively change its surface oxidation state, in the absence of an external electric current.

Across 27 countries, Većkalov and Geiger et al. find that scientific consensus messaging on climate change is an effective, non-polarizing tool for changing misperceptions, beliefs and worry but not support for public action.

Understanding the human exposome is now possible with clinics, communities and cities acting as real-world testbeds to understand what drives human healthspan, resilience and flourishing.

Dengue is a major public health concern in the Americas, and the Caribbean can be a source for reintroduction and spread. Here, the authors use travel surveillance data and genomic epidemiology to reconstruct Dengue epidemic dynamics in the Caribbean from 2009-2022.

Wildlife hunting can support diets and socio-economic well-being in communities around the world, but overexploitation can have cascading ecosystem effects. This study examines socio-cultural, economic and landscape factors associated with wildlife hunting in tropical forests in Africa.

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.

Nitrogen monoxide at low concentrations can promote the formation of highly oxygenated organic molecules, which are crucial precursors to secondary organic aerosol (SOA), rather than inhibit it as traditionally thought.

Investigation of the chemical nature and sources of particulate matter at urban locations in four Chinese cities during a severe haze pollution event finds that the event was driven to a large extent by secondary aerosol formation.

Brazil has operated a conditional cash transfer program to support families living in precarious conditions since 2004. Here, the authors use linked administrative and health data to investigate the impacts of the program on HIV/AIDS-related outcomes, demonstrating strong positive associations.

This study presents the first annual update of the indicator framework developed by the Food Systems Countdown Initiative, published in Nature Food in 2023. Almost half of all indicators show some desirable trends. Governance and resilience indicators were revealed as the most connected across themes, constituting entry points for transformative change.

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.

Here the authors apply machine learning approaches to Alzheimer’s genetics, confirm known associations and suggest novel risk loci. These methods demonstrate predictive power comparable to traditional approaches, while also offering potential new insights beyond standard genetic analyses.

Holistic indicator frameworks are needed to track food systems transformation. This Analysis shows the application of a framework recently developed by the Food Systems Countdown Initiative to all UN member states, revealing current status, data gaps and priority actions.

For different future scenarios, end-of-century mortality could quadruple from present day values. Importantly, the non-optimal temperature attributable mortality will increase at faster rate than the air pollution one, making it a more important health risk factor than air pollution for at least 20% of the world’s population.

Warm and moist air-mass intrusions into the Arctic are more frequent than the past decades. Here, the authors show that warm air mass intrusions from northern Eurasia inject record amounts of aerosols into the central Arctic Ocean strongly impacting atmospheric chemistry and cloud properties.

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.

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.

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.

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.

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.

To protect millions from unnecessary power outages, utility companies need one thing above all: data.

Digital measurements of proximity and duration of exposure by the NHS COVID-19 app show a strong relation to actual infections among 7 million contacts notified in England and Wales, with longer durations translating to increased risk of transmission.

The Mass Spectrometry Query Language (MassQL) is an open-source language that enables instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills.