Search

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.

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.

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.

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.

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.

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.

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.

An immunocompetent liver-on-a-chip platform with a targeted cell depletion strategy identifies cell-type-specific contributions to drug-induced hepatotoxicity, advancing predictive toxicology.

Within-sibship genome-wide association analyses using data from 178,076 siblings illustrate differences between population-based and within-sibship GWAS estimates for phenotypes influenced by demographic and indirect genetic effects.

Photoacoustic imaging has generated increasing interest for uses in preclinical research and clinical translation. Here the authors develop a three-dimensional photoacoustic computed tomography system that allows for multipurpose imaging of biological tissues ranging from the rodent brain to the human breast.

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.

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.

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.

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.

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.

Disturbing the redox balance in anaerobic bacteria presents a promising but underdeveloped strategy for the treatment of difficult-to-cure diseases caused by anaerobic bacteria. Here, the authors report a photocatalytic system to perturb the redox balance in oxygen-free conditions, achieving photocatalytic therapy to treat periodontitis.

Both rare and common variants contribute to the aetiology of complex traits such as type 2 diabetes (T2D). Here, the authors examine the effect of coding variation on glycaemic traits and T2D, and identify low-frequency variation in GLP1Rsignificantly associated with these traits.

Soils may release more CO₂ under warming when increases in plant productivity mine nitrogen from soil organic matter, according to an analysis of a global dataset of soil organic carbon measurements.

Whole-genome sequencing of 3,171 cultivated and 195 wild chickpea accessions is used to construct a chickpea pan-genome, providing insight into chickpea evolution and enabling breeding strategies that could improve crop productivity.

Therapeutics delivery by using non-viral vectors presents several challenges in the design of an appropriate polymeric structure. Here, the authors report a series of highly branched, biodegradable polymers which show high transfection efficiency in human multipotent adipose derived stem cells and primary astrocytes.

Family-based study designs have been applied to resolve confounding by population stratification, dynastic effects and assortative mating in genetic association analyses. Here, Brumpton et al. describe theory and simulations for overcoming such biases in Mendelian randomization through within-family studies.

Protein-mediated transport is implicated in trafficking fatty acids at contact sites of lipid droplets and mitochondria. Here, the authors use proteomics to catalogue the proteins at this contact site and report a mechanism of fatty acid transfer that regulates fatty acid oxidation and lipid homeostasis.

Risk prediction for prognosis in colorectal cancer is an important tool. Here, the authors utilise GWAS from 5 cohorts of colorectal cancer patients, and show a healthy lifestyle is associated with a 7.6% improvement in overall survival among patients with high pathologic and genetic risk.

The American cockroach (Periplaneta americana) is an hemimetabolous insect with rapid growth, high fecundity, and remarkable tissue-regeneration capability. Here Li et al sequence its 3.38-Gb genome and perform the functional studies, yielding insights into its environmental adaptation and developmental plasticity.

Two chiral enantiomers, R- and S-BBTI, are found to efficiently emit near-infrared circularly polarized phosphorescence with a large dissymmetry factor of 0.013 in dilute solutions.

Optical pooled CRISPR screening is improved by combinatorial oligo hybridization for barcode detection.

This study demonstrates the Coulomb focusing in nonadiabatic tunneling ionization inducing the convergence of electrons emitted at different initial ionization times to the same emission angle, thereby breaking the one‐to-one correspondence—one of the fundamental assumption in attosecond angular streaking.

Scientists have gained a fundamental insight into the ultrafast dynamics in nanoplasma formation and relaxations, yet the effective control on the emission behaviors of nanoplasma, is still lacking. Here, the authors report the experimental realization of well-controlled ion emission from transient nanoplasmas induced by intense femtosecond laser pulses.

A third dose of an mRNA vaccine against SARS-CoV-2 results in an expanded B cell repertoire that produces antibodies with increased potency and breadth.

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.

Glioblastoma stem cells co-opt lysine uptake and degradation to shunt the production of crotonyl-CoA, remodelling the chromatin landscape to evade interferon-induced intrinsic effects on glioblastoma stem cell maintenance and extrinsic effects on immune response.

Hydrophobic interactions occur between nonpolar molecules in water and their experimental quantification can help the understanding of biological self-assembly. Here Jianget al. examine the kinetics and thermodynamics of hydrophobic aggregation in a bulk environment and characterize its cooperativity.

Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

Efficient, large-scale genomic analysis is facilitated on the cloud by a computational tool with error-diagnosing and self-healing capabilities.

The development of intelligent materials, in particular those showing the highly sensitive mechanoresponsive luminescence (MRL), remains challenging. Here the authors report a strategy for constructing high performance On-Off MRL materials by introducing nitrophenyl groups to molecules with aggregation-induced emission characteristic.

The demonstration of pure organic room temperature phosphorescence (RTP) luminogens with complementary emission is a key requirement for developing low-cost white light emitters. Here, the authors construct RTP-active organic salt compounds by exchanging the counterion with a heavy halide ion.

The development of single molecule white light-emitters is extremely challenging for pure phosphorescent metal-free systems at room temperature. Here the authors show a single pure organic room temperature phosphor, 4-chlorobenzoyldibenzothiophene, utilizing the emission from both T₁ and T₂ states.