Genetic variation articles within Nature Reviews Genetics

Featured

  • Research Highlight |

    Logsdon et al. report the second complete sequence of all centromeres from a single human genome, enabling comparative analyses of the variation in tandemly repeating α-satellite DNA.

    • Kirsty Minton

  • Comment |

    In this Comment, Lamkin and Gymrek discuss recent results that suggest that the systematic incorporation of tandem repeats into complex trait analyses will yield a rich source of causal variants and new biological insights.

    • Michael Lamkin
    •  & Melissa Gymrek

  • Review Article |

    Genetic variants acquired early during embryogenesis can affect numerous tissues. The authors review the phenomenon of embryonic mosaicism, with a focus on small variants, and discuss mechanisms of cell competition that allow mosaic clones to expand, as well as the functional consequences of mosaicism for embryo viability and the health of the organism.

    • Sarah M. Waldvogel
    • , Jennifer E. Posey
    •  & Margaret A. Goodell

  • Review Article |

    In this Review, the authors compare the characteristics and detection methods of germline and somatic variants. Furthermore, they outline how the interplay between the two types of genetic variation can affect human health.

    • Zhi Yu
    • , Tim H. H. Coorens
    •  & Pradeep Natarajan

  • Journal Club |

    Reflecting on the importance of short tandem repeats (STRs) in population genetics, Ning Xie highlights a 2023 publication that characterized genome-wide STR variation in global human genomes to expand our understanding of STR genetic diversity within and across populations.

    • Ning Xie

  • Research Highlight |

    A publication in Nature reports the data release of around 245,000 clinical-grade whole-genome sequences as part of the NIH’s All of Us Research Programme. Several companion papers highlight the value of better capturing global genomic diversity.

    • Linda Koch

  • Journal Club |

    In this Journal Club, Yoav Ram recalls how he reconciled results from his own research with the reduction principle through the help of a paper published in PNAS by Altenberg et al.

    • Yoav Ram

  • Review Article |

    In this Review, Sayers et al. summarize findings from recent large-scale genetic epidemiology studies on the genetic underpinnings of chronic respiratory diseases. Furthermore, they outline how insights gained from such studies can improve treatment approaches.

    • Ian Sayers
    • , Catherine John
    •  & Ian P. Hall

  • Review Article |

    Plant pangenomes have had a transformative impact on crop enhancement, biodiversity conservation and evolutionary research. This Review delves into the application of plant pangenomes for understanding trait diversity, aiding breeding, biodiversity classification and monitoring, and illuminating evolutionary innovations.

    • Mona Schreiber
    • , Murukarthick Jayakodi
    •  & Martin Mascher

  • Review Article |

    This Review describes tools and approaches for characterizing short tandem repeats in the human genome from whole-genome sequencing data. Furthermore, the authors discuss how these recent developments have helped to better understand the effect of short tandem repeats on human health and disease.

    • Hope A. Tanudisastro
    • , Ira W. Deveson
    •  & Daniel G. MacArthur

  • Research Highlight |

    Four papers in Nature describe how ancient European migration patterns have shaped the modern human genome.

    • Michael Attwaters

  • Review Article |

    Species and communities can respond to global climate change by genetically adapting to new environmental conditions, by shifting their range or through phenotypic plasticity. This Review summarizes approaches that apply and integrate omics tools to experimentally investigate, monitor and predict these species responses.

    • Louis Bernatchez
    • , Anne-Laure Ferchaud
    •  & Amanda Xuereb

  • Journal Club |

    Luis Barreiro highlights a 2007 paper by Tishkoff et al. that identified genetic variants associated with lactose persistence in East African populations, representing one of the first examples of convergent evolution in humans.

    • Luis B. Barreiro

  • Review Article |

    Ancient DNA studies over the past decade have yielded a plethora of insights into the Denisovan archaic hominin group. The authors review our understanding of Denisovan population history and their interactions with other human groups, insights from studies of Denisovan ancestry in modern humans, what we know about the Denisovan phenotype and their impact on our own evolutionary history.

    • Stéphane Peyrégne
    • , Viviane Slon
    •  & Janet Kelso

  • Review Article |

    Applying deep learning to large-scale genomic data of species or populations is providing new opportunities to understand the evolutionary forces that drive genetic diversity. This Review introduces common deep learning architectures and provides comprehensive guidelines to implement deep learning models for population genetic inference. The authors also discuss current opportunities and challenges for deep learning in population genetics.

    • Xin Huang
    • , Aigerim Rymbekova
    •  & Martin Kuhlwilm

  • Review Article |

    This Review summarizes the genetic and non-genetic factors that impact the transferability of polygenic risk scores (PRSs) across populations, highlighting the technical challenges of existing PRS construction methods for diverse ancestries and the emerging resources for more widespread use of PRSs.

    • Linda Kachuri
    • , Nilanjan Chatterjee
    •  & Tian Ge

  • Research Highlight |

    In five new studies, the Human Pangenome Reference Consortium reports the generation and initial characterization of a draft human pangenome.

    • Michael Attwaters

  • Journal Club |

    Tanja Woyke highlights a 2014 study by Kashtan et al., who applied single-cell genomics to populations of the marine cyanobacterium Prochlorococcus, revealing hundreds of subpopulations with distinct genomic backbones of this wild uncultured microorganism.

    • Tanja Woyke

  • Journal Club |

    Sophie von der Heyden highlights a paper by Barber et al. that examined variations in the genetic structuring of populations of the mantis shrimp Haptosquilla pulchella, furthering our understanding of the evolutionary dynamics of marine species.

    • Sophie von der Heyden

  • Review Article |

    Variant calling is the process of identifying genetic variants, which is important for characterizing population genetic diversity and for identifying disease-associated variants in clinical sequencing projects. In this Review, the authors discuss the state-of-the-art in variant calling, focusing on challenging types of genetic variants, advances in both sequencing technologies and computational pipelines, and benchmarking strategies to assess the robustness of variant-calling strategies.

    • Nathan D. Olson
    • , Justin Wagner
    •  & Justin M. Zook

  • Review Article |

    This Review discusses the importance of understanding the mechanisms by which specific allelic variants and allelic combinations cause disease for accurately diagnosing, treating and counselling individuals with genetic disorders.

    • Johannes Zschocke
    • , Peter H. Byers
    •  & Andrew O. M. Wilkie

  • Research Highlight |

    A comparative genomics study published in Nature Communications provides new insight into the genomic changes underlying the convergent evolution of sociality in spiders.

    • Dorothy Clyde

  • Research Highlight |

    A study in Nature reports the identification of new germline variants associated with particular subtypes of clonal haematopoiesis of indeterminate potential (CHIP) and their links to different health outcomes.

    • Kirsty Minton

  • In Brief |

    A paper in Nature Communications describes a framework for identifying seed traits in food crops that have health-promoting effects on the gut microbiome, with implications for crop improvement approaches.

    • Dorothy Clyde

  • Journal Club |

    In this Journal Club article, María Ávila-Arcos discusses a paper on a medically relevant genetic variant that was found exclusively in Indigenous populations from the Americas. She describes how this work served as inspiration for the inclusion of more diverse populations in the 1000 Genomes Project.

    • María C. Ávila-Arcos

  • Research Highlight |

    A new study in Cell has characterized genome-wide dosage sensitivity for 54 human disorders, providing insight into the causal genes and disease mechanisms associated with rare copy-number variants.

    • Dorothy Clyde

  • Research Highlight |

    Two new papers in Nature report copy-number-based classification systems across cancer types that provide routes for personalized therapy.

    • Darren J. Burgess

  • Review Article |

    In this article, Niemi, Daly and Ganna discuss how large-scale genomics studies are providing a rapidly maturing understanding of the influence of host genetics on coronavirus disease 2019 (COVID-19) susceptibility and severity. They also describe the implications for identifying causal mechanisms of pathology and potential therapeutic opportunities.

    • Mari E. K. Niemi
    • , Mark J. Daly
    •  & Andrea Ganna

  • Journal Club |

    In this Journal Club, Yukinori Okada recalls a 1987 publication that introduced a simple conceptual framework, the shared epitope hypothesis, to explain the genetic risk of rheumatoid arthritis conferred by HLA-DRB1 alleles.

    • Yukinori Okada

  • Journal Club |

    In this Journal Club, Itai Yanai discusses key quantitative work characterizing the occurrence and fates of gene duplicates across various species.

    • Itai Yanai

  • In Brief |

    A study in eLife identifies 71 nuclear loci associated with mitochondrial DNA copy number (mtDNA-CN) and reveals a putative causal role for mtDNA-CN in dementia.

    • Dorothy Clyde

  • Journal Club |

    In this Journal Club article, Fowzan Alkuraya describes how a paper outlining the mathematical foundations of homozygosity mapping provided a route to disease gene identification that still benefits his patients in clinical practice today.

    • Fowzan S. Alkuraya

  • Review Article |

    In this Review, Loos and Yeo summarize our current understanding of the genetic underpinnings of monogenic and polygenic obesity. They highlight the commonalities revealed by recent studies and discuss the implications for treatment and prediction of obesity risk.

    • Ruth J. F. Loos
    •  & Giles S. H. Yeo

  • Research Highlight |

    This molecular phenotyping study shows that common variants in mitochondrial DNA associated with diseases of ageing influence cellular protein homeostasis, and that this link is mediated by circulating levels of N-formylmethionine, the initiating amino acid in mitochondrial protein synthesis.

    • Caroline Barranco

  • Review Article |

    Leigh and colleagues describe the potential of the emerging field of macrogenetics to improve conservation and biodiversity management. Challenges preventing the field from reaching its full promise are highlighted and possible solutions and a framework for future macrogenetic studies are proposed.

    • Deborah M. Leigh
    • , Charles B. van Rees
    •  & Ivan Paz-Vinas

  • In Brief |

    A recent study has analysed publicly available long-read sequencing data to characterize human-specific variable number tandem repeats at high resolution.

    • Linda Koch

  • Research Highlight |

    Capturing rare protein-coding variation by whole-exome sequencing in large and diverse population samples can help identify large-effect associations and drug targets, suggest two recent publications.

    • Linda Koch

  • In Brief |

    A study in the American Journal of Human Genetics shows that using the GRCh37 versus GRCh38 version of the human reference genome makes a meaningful difference to the calling of human genetic variants, with implications for research-based and clinical-based human sequencing studies.

    • Darren Burgess

  • Review Article |

    McLaren and Fellay review our current understanding of the effects of human genetic variation on HIV infection and disease progression and how this knowledge is contributing to preventative and therapeutic approaches.

    • Paul J. McLaren
    •  & Jacques Fellay

  • Comment |

    Variants in mitochondrial DNA (mtDNA), which are detectable in whole-genome sequencing (WGS) data, can cause a wide range of phenotypes of varying severity. The authors call for a wider debate on the communication of uncertainties around mtDNA variants and the risks versus benefits of screening.

    • William L. Macken
    • , Anneke M. Lucassen
    •  & Robert D. S. Pitceathly

  • Research Highlight |

    Two studies co-published in Nature Genetics describe induced pluripotent stem cell-based resources for identifying novel, disease-related genetic variants.

    • Joseph Willson

  • 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

  • In Brief |

    The TOPMed consortium report whole-genome sequencing data from 53,831 ethnically diverse participants. They describe the key features of the genetic variation and produce data resources for future medical research by the wider scientific community.

    • Darren J. Burgess

  • In Brief |

    In this paper in Nature Genetics, Atkinson et al. describe Tractor, a statistical framework and software package that enables admixed populations to be included in large-scale genomics studies.

    • Dorothy Clyde

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