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This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

There are various — and confusing — targets to limit global warming due to emissions of greenhouse gases. Estimates based on the total slug of carbon emitted are possibly the most robust, and are worrisome.

The world may be largely indifferent to the presence of humanity, yet we have magnified our influence to global scales - above all, through the recent increase in atmospheric greenhouse gases.

The equilibrium response of global temperatures to an increase in atmospheric carbon dioxide concentrations is difficult to quantify. Simulations and proxy data of the mid-Pliocene warm climate suggest that the response is 30 to 50% higher than traditionally calculated when slowly adjusting components of the Earth system, such as ice sheets and vegetation, are included in the estimate.

The demise of the Laurentide ice sheet during the early Holocene epoch allows rates of ice sheet decay under natural conditions to be assessed. Analysis of terrestrial and marine records of the deglaciation along with a climate model reveal two periods of rapid melting during the final retreat of this ice sheet, with rates of sea level rise of up to 1.3 cm per year.

Taking into account all known factors, the planet warmed 0.2 °C more last year than climate scientists expected. More and better data are urgently needed.

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

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.

It is important to know how the recent COVID-19 pandemic shaped the immune memory against the causal SARS-CoV-2 virus. Here authors show that long years following mild disease at primary infection, SARSCoV-2 spike-specific CD4 + T cells with distinct phenotypes and T cell receptor clonotypes, associated with viral suppression persist.

Scientists know much more about their field than is ever published in peer-reviewed journals. Blogs can be a good medium with which to disseminate this tacit knowledge.

Observations from a borehole in the Kamb Ice Stream suggest that discrete subglacial discharge events dominate channel melt and sediment transport.

Maatz, Lindberg et al. identify molecular alterations and immune response changes in endomyocardial biopsies from patients with myocarditis after COVID-19 infection, after anti-COVID-19 vaccination or from non-COVID-related causes.

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.

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.

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.

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.

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.

Although intraspecific dominance hierarchies are common, large scale interspecific dominance hierarchies are unknown. Using data from hundreds of avian species, the authors find that species that are more familiar with each other engage in less aggression and the aggression is resolved more directly.

Reduced glomerular filtration rate (eGFR) is a hallmark of chronic kidney disease. Here, Pattaro et al. conduct a meta-analysis to discover several new loci associated with variation in eGFR and find that genes associated with eGFR loci often encode proteins potentially related to kidney development.

The response of climate to external forcing is known as climate sensitivity, and its estimates are calculated from historical observations. This study estimates the efficacy of individual forcings and revises climate sensitivities accordingly.

Despite an increase in solar output, the Earth’s climate has apparently remained relatively stable over geological time. Here, the authors compile atmospheric CO₂data for the past 420 million years and show that this climatic response is due to the long-term decline in this powerful greenhouse gas.

Known genetic loci account for only a fraction of the genetic contribution to Alzheimer’s disease. Here, the authors have performed a large genome-wide meta-analysis comprising 409,435 individuals to discover 6 new loci and demonstrate the efficacy of an Alzheimer’s disease polygenic risk score.

The uterine scar that results from cesarean surgery is associated with placenta accreta spectrum (PAS) during subsequent pregnancies. Here, the authors created a model of uterine scar and show that scar matrix activates mechanosensitive ion channel, Piezo1, which causes  inflammatory transformation of the decidua, leading to recruitment of extravillous trophoblasts towards the scar, thereby initiating PAS.

Researchers developed an accurate model to analyse bivalent antibody binding. By analysing many SARS-CoV-2-specific antibodies, they found that their molecular reach can predict their neutralisation potency.

Engineering efforts have focused on acyltransferase (AT) domains of modular polyketide synthases (PKSs) to site-selectively modify the resulting polyketides, but critical AT residues involved in substrate selection have not been fully elucidated. Here, the authors use molecular dynamics to pinpoint mutations that impact AT domain selectivity and exchange structural motifs to obtain chimeric PKS modules with expanded substrate specificity.

Global mean surface and tropospheric temperatures have shown slower warming since 1998 than found in climate model simulations. A detailed analysis of observations and climate model simulations suggests that the observed influence of volcanic eruptions on tropospheric temperature has been significant, and that the discrepancy between climate simulations and observations is reduced by up to 15% when twenty-first century volcanic eruptions are accounted for in the models.

Current thinking on the causes of anthropogenic radiative forcing in the lower atmosphere is misleading. This study finds tropospheric ozone-precursor emissions have contributed more to positive forcing, and halocarbons more to negative forcing, than previously thought.

The authors characterize immune response in Omicron-infected vaccinated individuals and observe an immune enhancement. While increases in neutralizing antibodies and spike T cells are stronger in previously naïve individuals, mucosal antibodies and non-spike responses increase regardless of infection history.

A possible kilonova associated with a nearby, long-duration gamma-ray burst suggests that gamma-ray bursts with long and complex light curves can be spawned from the merger of two compact objects, contrary to the established gamma-ray burst paradigm.

Paul Elliott, Martin Tobin, Cornelia van Duijn and colleagues report a genome-wide association study for pulse pressure and mean arterial pressure, identifying six new loci influencing these two traits.