Health sciences articles within Nature Reviews Genetics

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  • Perspective |

    In this Perspective article, Oh and Petronis discuss emerging evidence of time-dependent patterns of DNA modification and describe how incorporating this ‘chrono-epigenetic’ perspective could add value and interpretability in human disease studies.

    • Edward Saehong Oh
    •  & Art Petronis

  • Journal Club |

    Cisca Wijmenga reflects on a seminal publication by Houwen et al. that set the stage for genome-wide association studies and inspired her to dedicate her lab to complex trait genetics.

    • Cisca Wijmenga

  • Review Article |

    In this Review, Neafsey, Taylor and MacInnis discuss how population genomics approaches are currently used to study malaria parasites and mosquito vectors. They explore information that can be derived from such genomics approaches and discuss the use of relatedness-based measures of population variation to understand parasite and vector dynamics at highly resolved spatiotemporal scales.

    • Daniel E. Neafsey
    • , Aimee R. Taylor
    •  & Bronwyn L. MacInnis

  • Review Article |

    Profiling tumours by next-generation sequencing can improve diagnostic accuracy, assess for heritable cancer risk and guide treatment selection. The authors review efforts to enhance the clinical utility of cancer genomic profiling through integrative analyses of tumour and germline variants, as well as by characterizing allelic context and mutational signatures that influence therapy response.

    • Debyani Chakravarty
    •  & David B. Solit

  • Research Highlight |

    Two new studies in Cell report the use of CRISPR–Cas cytosine base editors (CBEs) in mammalian cells for high-throughput functional genomics screens.

    • Linda Koch

  • Research Highlight |

    Two new papers in Nature Biotechnology report methods for targeted sequencing of complex DNA samples, achieved in real time during nanopore sequencing runs.

    • Darren J. Burgess

  • In Brief |

    Jin et al. describe a barcoding approach for analysing metastasis, which they used to generate an organ-specific metastasis map for 500 cancer cell lines.

    • Dorothy Clyde

  • In Brief |

    Fozouni et al. describe a CRISPR–Cas13a-based approach for rapid, accurate and portable detection of SARS-CoV-2 in infected individuals.

    • Dorothy Clyde

  • Research Highlight |

    Two new reports in Cell use genome-wide CRISPR screens to uncover host determinants of coronavirus infection, identifying potential leads for antiviral therapeutics.

    • Darren J. Burgess

  • Research Highlight |

    The GTEx consortium reports results from its third and final phase in several new papers. They provide unprecedented detail of human gene expression regulation across tissues.

    • Darren J. Burgess

  • Research Highlight |

    Two papers in Cell report large-scale genome-wide association studies that provide new insights into the genetic architecture of haematopoietic phenotypes and emphasize the importance of large, diverse data sets.

    • Dorothy Clyde

  • Research Highlight |

    A new study in Science uses chromatin accessibility profiles to reveal gene regulatory alterations associated with genetic variants in neuropsychiatric disease.

    • Darren J. Burgess

  • Review Article |

    This Review outlines a broad, universal framework for systems biology applied to infectious disease research. From study design and omics data collection, analysis, visualization and interpretation to translational outcomes, the authors illustrate how systems biology can provide insights into host–pathogen relationships for the betterment of human health.

    • Manon Eckhardt
    • , Judd F. Hultquist
    •  & Nevan J. Krogan

  • Comment |

    Direct-to-consumer epigenetic tests have the potential to reveal sensitive information about individuals, such as disease risk and exposure history. Yet regulation lags behind purely genetics-based tests. In this Comment article, the authors discuss the salient ethical and legal considerations of direct-to-consumer epigenetic tests.

    • Charles Dupras
    • , Elisabeth Beauchamp
    •  & Yann Joly

  • Research Highlight |

    A recent study in Nature Microbiology reports metagenomic signatures of early-life antibiotic treatment and hospitalization associated with preterm birth that persist long-term.

    • Linda Koch

  • Review Article |

    Somatic genetic rescue (SGR) occurs when an acquired somatic mutation counteracts the effects of a germline mutation at a cellular level. The increasing number of SGR events reported for Mendelian haematopoietic diseases have important diagnostic, therapeutic and clinical consequences.

    • Patrick Revy
    • , Caroline Kannengiesser
    •  & Alain Fischer

  • Research Highlight |

    Two recent studies trace epigenetic marks in cells from patients with chronic lymphocytic leukaemia (CLL) to characterize the evolution of the epigenome in cancer.

    • Carolina N. Perdigoto

  • Review Article |

    This Review discusses the current status of expanded carrier screening, including existing recommendations and limitations. The author reviews the framework that is needed for successful comprehensive carrier screening programmes for all autosomal recessive disorders in various populations.

    • Stylianos E. Antonarakis

  • Editorial |

    Genomics has transformed the field of microbiology, but remaining challenges will need to be tackled for its benefits to be felt globally.

  • Review Article |

    Despite the success of human genome-wide association studies (GWAS) in associating genetic variants and complex diseases or traits, criticisms of the usefulness of this study design remain. This Review assesses the pros and cons of GWAS, with a focus on the cardiometabolic field.

    • Vivian Tam
    • , Nikunj Patel
    •  & David Meyre

  • Research Highlight |

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

    • Linda Koch

  • Review Article |

    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.

    • Maria A. Spyrou
    • , Kirsten I. Bos
    •  & Johannes Krause

  • Comment |

    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.

    • Noor A. A. Giesbertz
    • , Wim H. van Harten
    •  & Annelien L. Bredenoord

  • Review Article |

    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.

    • Charles Y. Chiu
    •  & Steven A. Miller

  • Review Article |

    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.

    • Manish Boolchandani
    • , Alaric W. D’Souza
    •  & Gautam Dantas

  • Comment |

    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.

    • Stephanie B. Johnson
    •  & Michael Parker

  • Research Highlight |

    The BabySeq project, a pilot randomized clinical trial exploring the value of routine genomic sequencing of neonates compared with standard newborn screening, now reports initial results in the American Journal of Human Genetics.

    • Linda Koch

  • Comment |

    This Comment discusses how data from smartphones or wearables could be used for behavioural phenotyping, knowledge that may help to reveal the genetic and environmental contributions to disease-related behavioural variation.

    • Nelson B. Freimer
    •  & David C. Mohr

  • Comment |

    The lack of family health history experienced by most adopted persons can represent a marked disadvantage for these individuals. Genetic testing has the potential to reliably and usefully fill informational gaps, but considerable challenges need to be addressed to assemble an economic case for affordability.

    • Thomas May

  • Comment |

    In personalized medicine, a major aim is to provide the right treatment to the right patient. In this Comment article, Gibson discusses how a more overt and genomics-informed focus on those individuals who are unlikely to benefit from treatment could reduce prescription rates and provide financial and health-care benefits.

    • Greg Gibson

  • Research Highlight |

    Two studies in Nature describe the full data set of the UK Biobank resource, which contains genome-wide genetic data, clinical measurements and health records for ~500,000 individuals, and reveal insights into the brain’s genetic architecture.

    • Orli G. Bahcall

  • Comment |

    Genome-wide sequencing (GWS) is the most sensitive test available for detecting pathogenic genetic variants but it generates complex results. It is important, therefore, that individuals undergoing GWS are offered both pre-test and post-test genetic counselling.

    • Alison M. Elliott
    •  & Jan M. Friedman

  • Review Article |

    Various types of observational studies can provide statistical associations between factors, such as between an environmental exposure and a disease state. This Review discusses the various genetics-focused statistical methodologies that can move beyond mere associations to identify (or refute) various mechanisms of causality, with implications for responsibly managing risk factors in health care and the behavioural and social sciences.

    • Jean-Baptiste Pingault
    • , Paul F. O’Reilly
    •  & Frank Dudbridge

  • Comment |

    Current approaches for diagnosing mitochondrial disorders involve specialist clinical assessment, biochemical analyses and targeted molecular genetic testing. There is now a strong rationale for undertaking first-line genome-wide sequencing, accelerating the speed of diagnosis and avoiding the need for expensive and invasive investigations.

    • F. Lucy Raymond
    • , Rita Horvath
    •  & Patrick F. Chinnery

  • Review Article |

    Parallels are increasingly being drawn between prion diseases and other aggregate-mediated neurodegenerative disorders. While prion diseases are a distinct subclass of protein misfolding disorders (PMDs), a better understanding of shared mechanisms is likely to benefit treatment of all PMDs.

    • Claudia Scheckel
    •  & Adriano Aguzzi

  • Review Article |

    Biomarkers of ageing based on DNA methylation data enable accurate age estimates for any tissue across the entire life course. Horvath and Raj review the development of these ‘epigenetic clocks’ and how they link to biological ageing.

    • Steve Horvath
    •  & Kenneth Raj

  • Comment |

    A recent patent granted for methods for diagnosing autism spectrum disorder (ASD) raises several ethical concerns beyond the fundamental question of whether genomic sequences are patentable, as it suggests that genetic testing can provide a diagnosis of ASD even before behavioural symptoms present.

    • Kristien Hens
    • , Ilse Noens
    •  & Jean Steyaert

  • Review Article |

    DNA repeats are more liable to mutation than other genetic variants, which enables them to mediate genetic plasticity. The expansion of tandem repeats can cause a range of monogenic disorders, contribute to the missing heritability of polygenic disorders and regulate gene expression, as well as RNA and protein function, in healthy individuals.

    • Anthony J. Hannan

  • Review Article |

    The emerging field of paediatric genomics has leveraged the power of next-generation sequencing technologies to improve the diagnostic rates of rare disease in children. This Review addresses key considerations for safe and effective implementation of genomics in the clinic.

    • Caroline F. Wright
    • , David R. FitzPatrick
    •  & Helen V. Firth

  • Review Article |

    Although cancer genome sequencing is becoming routine in cancer research, cancer transcriptome profiling through methods such as RNA sequencing (RNA-seq) provides information not only on mutations but also on their functional cellular consequences. This Review discusses how technical and analytical advances in cancer transcriptomics have provided various clinically valuable insights into gene expression signatures, driver gene prioritization, cancer microenvironments, immuno-oncology and prognostic biomarkers.

    • Marcin Cieślik
    •  & Arul M. Chinnaiyan

  • Review Article |

    Genetic architecture describes the characteristics of genetic variation that are responsible for phenotypic variability. This Review discusses the types of genetic architecture that have been observed, how they can be measured and how genetic architecture informs the scientific and clinical goals of human genetics.

    • Nicholas J. Timpson
    • , Celia M. T. Greenwood
    •  & J. Brent Richards

  • Review Article |

    Next-generation sequencing has the potential to support public health surveillance systems to improve the early detection of emerging infectious diseases. This Review delineates the role of genomics in rapid outbreak response and the challenges that need to be tackled for genomics-informed pathogen surveillance to become a global reality.

    • Jennifer L. Gardy
    •  & Nicholas J. Loman

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