Articles in 2019

Two meta-analyses of fecal metagenomics studies report the presence of a microbial signature that is predictive of colorectal cancer.

This Review describes different deep learning techniques and how they can be applied to extract biologically relevant information from large, complex genomic data sets.

A fuller understanding of bacterial genomic variation could provide insight into host pathophysiology. A new study in Nature demonstrates that structural variants are highly prevalent in human gut microbiomes and that some associate with host disease risk factors.

This article reviews recent advances in ancient pathogen genomics, from methodological improvements in retrieving whole genomes to evolutionary analyses of ancient pathogens that remain relevant to public health. Focusing on the evolutionary history of the plague pathogen Yersinia pestis, the authors present unique insights afforded by the study of ancient pathogen genomes.

A new study in Science reports the existence of a subpopulation of somatic cells from which ‘elite’ clones emerge that outperform other clones to drive reprogramming.

The clinical application of genomic technologies is driving new discoveries that may be relevant to individuals who have previously undergone genetic testing. This Comment highlights the need for a framework to decide whether to recontact patients and inform them of new genetic findings.

In a study in Nature Microbiology, Setoh et al. use deep mutational scanning to speed up viral evolution and identify key determinants of host tropism in Zika virus.

Recent next-generation sequencing studies have captured the spatial and temporal evolutionary patterns that shape cancer. This Review provides an overview of the theoretical models of tumour evolution and discusses what to consider when inferring evolutionary dynamics from genomic data.

Clinical metagenomic next-generation sequencing (mNGS) is rapidly moving from bench to bedside. This Review discusses the clinical applications of mNGS, including infectious disease diagnostics, microbiome analyses, host response analyses and oncology applications. Moreover, the authors review the challenges that need to be overcome for mNGS to be successfully implemented in the clinical laboratory and propose solutions to maximize the benefits of clinical mNGS for patients.

Two recent articles in Nature Reviews Genetics discuss the exciting opportunities of single-cell omics studies but also highlight the importance of appropriate data analysis strategies.

Two studies report substantial temporal and spatial variability in mutagenic signatures caused by APOBEC cytidine deaminases in cancer.

A study in Nature reveals that N⁶-methyladenosine (m⁶A) modification of RNA occurs co-transcriptionally and is mediated by interactions between histone H3 lysine 36 trimethylation (H3K36me3) and the m⁶A methyltransferase complex.

Nair et al. contrast events at specific super-enhancers after acute and chronic ligand-induced activation and show that biomolecular condensates at these enhancers undergo physical changes over time that affect chromatin conformation and gene expression.

Using the example of carbon concentrating mechanisms in plants, the authors of this Perspective provide evidence that broad comparative genomic analyses likely overestimate the genetic complexity underlying convergent evolution of complex traits.

Eukaryotes differ substantially from bacteria and archaea owing to their nucleosome-based packaging of DNA. In this Review, Talbert, Meers and Henikoff place gene regulation in an evolutionary context by discussing how the emergence and diversification of eukaryotic chromatin provided both challenges and opportunities for intricate mechanisms of gene regulation in eukaryotes.

Next-generation sequencing has improved the identification and characterization of antimicrobial resistance. Focusing on sequence-based discovery of antibiotic resistance genes, this Review discusses computational strategies and resources for resistance gene identification in genomic and metagenomic samples, including recent deep-learning approaches.

A genomics-informed response to infectious disease has great potential to improve individual patient treatment as well as public health. This Comment discusses the ethical, legal and social challenges that will need to be overcome if clinical pathogen genomics is to be implemented successfully.

Variants of unknown significance (VUS) are genetic variants whose association with disease risk is unknown. The authors posit that VUS should not inform clinical decision-making as the benefits of returning this genetic information to patients undergoing genetic testing are outweighed by the potential for harm.

Two studies in Science show that cytosine base editors, but not adenine base editors or CRISPR–Cas9, induce notable off-target single-nucleotide variants in rice and in mouse embryos.