Search

A microfluidic-based system enables fast screening of Mycobacterium tuberculosis infection through analysis of specific T-cell responses.

The authors present a chip-less wearable sensor-processor integrated neuromorphic system that combines multimodal physicochemical sensing with neuromorphic processing for real-time, autonomous physiological monitoring.

A large nuclear spin has been successfully placed in a Schrödinger cat state, a superposition of its two most widely separated spin coherent states. This can be used as an error-correctable qubit.

An integrated smart capsule that encapsulates an array of electrochemical sensors can provide real-time, continuous and multiplexed monitoring of the gastrointestinal tract.

Sepsis may promptly develop into lethal organ failure, so early diagnosis and treatment planning are essential. Here the authors use machine learning to develop a six-gene signature, termed Sepset, for initial diagnosis, and integrate Sepset into a microfluidic-based bench-side platform for predicting the prognosis of suspected sepsis suitable for the clinic.

Recent work explored the connection between quantum thermalization in closed many-body systems and classical chaos by projecting quantum dynamics onto classical dynamics. Here the authors further this understanding by analytically linking entanglement growth to the Lyapunov spectrum.

CMOS-based circuits can be integrated with silicon-based spin qubits and can be controlled at milli-kelvin temperatures, which can potentially help scale up these systems.

It is challenging to treat emerging organic contaminants such as pharmaceutical compounds. Using the proposed plant-based zirconium–ellagate framework, this study demonstrates high removal efficiencies of emerging organic contaminants from real untampered municipal wastewater treatment plant effluent.

Fluorinated elastomers as photoresists in the fabrication of soft neural probes are used to enhance the spatiotemporal recording capability at single-neuron resolution within the central nervous system of rodents.

Major histocompatibility complex (MHC) loss of heterozygosity, allele-specific mutation and measurement of expression and repression (MHC Hammer) detects disruption to human leukocyte antigens due to mutations, loss of heterogeneity, altered gene expression or alternative splicing. Applied to lung and breast cancer datasets, the tool shows that these aberrations are common across cancer and can have clinical implications.

Anisotropic spin S >1/2 quantum magnets can have multiple low energy modes. In this manuscript, the authors study the interaction of such low energy modes in the S = 1 antiferromagnet Ba₂FeSi₂O₇ by combining neutron scattering measurements with an SU(3) generalization of the 1/S expansion.

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.

The genomic features of precursor conditions of multiple myeloma provide multiple biological insights into disease origins and evolution, together with opportunities to identify those at highest risk of progression.

Analyses of multiregional tumour samples from 421 patients with non-small cell lung cancer prospectively enrolled to the TRACERx study reveal determinants of tumour evolution and relationships between intratumour heterogeneity and clinical outcome.

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

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.

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.

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.

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.

Smoking-associated DNA methylation changes in whole blood have been reported by many EWAS. Here, the authors use a cell-type deconvolution algorithm to identify cell-type specific DNA methylation signals in seven EWAS, identifying lineage-specific smoking-associated DNA methylation changes.

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.

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.

Genomic and functional analysis of intratumor heterogeneity in pediatric glioma uncovers early clonal divergence and stable spontaneous cooperation between subclonal populations throughout tumor evolution.

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.

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.

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.

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 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.

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.

Determining whether somatosensory neurons are involved in internal or external sensing remains a challenge. Here, the authors show that analyzing connectivity is a powerful approach to identify putative neural functions of somatosensory neurons in the fly.

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.

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.

Combinatorial experimental and bioinformatics methods can be used to analyse function and specificity of CD8 T cells. Here the authors propose a multiomic analysis framework Antigen-TCR Pairing and Multiomic Analysis of T cell (APMAT) to relate TCR specificity to transcriptomic phenotype indicating associations with physicochemical features.

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.

Naylor et al. systematically review the efficacy of treatments for beta-cell monogenic diabetes. Limited evidence from the mostly non-randomized, small studies supports no treatment in glucokinase-related hyperglycemia and sulfonylureas for HNF1A-diabetes; further evidence is needed on the optimum treatments in these and other monogenic subtypes.

Using multi-ancestry genome-wide association study and fine-mapping, 298 loci and 36 credible genes are identified in the aetiology of bipolar disorder.

Silicon-based spin qubits are promising candidates for a scalable quantum computer. Here the authors demonstrate the violation of Bell’s inequality in gate-defined quantum dots in silicon, marking a significant advancement that showcases the maturity of this platform.

Metasurface alignment marks enable precise 3D measurement of relative positions of distant objects using only a laser and a camera, achieving sub-nanometer precision. Applications include 3D chips manufacturing and displacement sensors.

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.