Sequencing articles within Nature Reviews Genetics

Featured

  • Tools of the Trade |

    In this Tools of the Trade article, Samuel Gould explains how prime editing sensors can improve experimental efficiency and can be designed using a computational tool he created and named PEGG.

    • Samuel I. Gould

  • Journal Club |

    In this Journal Club, Kirstyn Brunker highlights two papers published in 2017 that showcase how the emergence of portable sequencing capabilities improved the real-time response to infectious disease outbreaks on a global scale.

    • Kirstyn Brunker

  • Review Article |

    In this Review, Li and Durbin discuss how to generate telomere-to-telomere assemblies for large haploid or diploid genomes using currently available data types and algorithms, and outline remaining challenges in resolving highly repetitive sequences and polyploid genomes.

    • Heng Li
    •  & Richard Durbin

  • Tools of the Trade |

    In this Tools of the Trade article, Dongsheng Bai and Chenxu Zhu describe SIMPLE-seq, a scalable single-cell sequencing method that simultaneously decodes the cytosine modifications 5mC and 5hmC.

    • Dongsheng Bai
    •  & Chenxu Zhu

  • 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

  • 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

  • Review Article |

    Genomic technologies have greatly improved the diagnosis of rare genetic diseases. Here, the authors review emerging approaches for the identification of disease-causal genetic variants as well as omic technologies that show great potential for variant interpretation.

    • Kristin D. Kernohan
    •  & Kym M. Boycott

  • Comment |

    Geopolitical instability has prompted renewed discussions on the risks of DNA technology being weaponized in international conflict. With today’s changing security environment, the authors argue that risk assessments must be broadened from genetically targeted weapons to a series of new domains.

    • Subhayan Chattopadhyay
    • , Tony Ingesson
    •  & David Gisselsson

  • Research Highlight |

    Guhlin et al. sequenced the genomes of almost the entire extant population of the critically-endangered kākāpō, revealing genetic variants for fitness-related traits that can inform conservation strategies.

    • Michael Attwaters

  • Research Highlight |

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

    • Michael Attwaters

  • Research Highlight |

    A study in Nature Biotechnology describes Scriabin, a highly scalable framework for inference of cell–cell communication from scRNA-seq data at the level of individual cells.

    • Dorothy Clyde

  • Journal Club |

    Marja Timmermans recalls a series of papers published back-to-back in Science in 2018 that reported the use of single-cell RNA sequencing to obtain a more complete picture of the expression landscapes describing early vertebrate development.

    • Marja C. P. Timmermans

  • Journal Club |

    In this Journal Club, Celine Vallot discusses two 2015 papers that introduced the concept of high-throughput RNA barcoding, which paved the way for today’s plethora of single-cell omic approaches.

    • Céline Vallot

  • 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

  • Research Highlight |

    A paper in Cell introduces the EN-TEx resource, a detailed catalogue of allele-specific activity that can be used to develop deep learning models that analyse the biological impact of genetic variants.

    • Linda Koch

  • Expert Recommendation |

    Practitioners in the field of single-cell omics are now faced with diverse options for analytical tools to process and integrate data from various molecular modalities. In an Expert Recommendation article, the authors provide guidance on robust single-cell data analysis, including choices of best-performing tools from benchmarking studies.

    • Lukas Heumos
    • , Anna C. Schaar
    •  & Fabian J. Theis

  • Research Highlight |

    Zhang et al. describe two technologies for the spatially resolved co-mapping of epigenome and transcriptome at near single-cell resolution.

    • Kirsty Minton

  • Journal Club |

    This journal club by Elisa Oricchio highlights two studies published in 2012, which used chromatin conformation capture methods to detect the formation of self-interacting chromatin regions, known as topologically associating domains (TADs).

    • Elisa Oricchio

  • Journal Club |

    Magda Bienko highlights a landmark paper by Lieberman-Aiden et al., which in 2009 reported the development of high-throughput chromosome conformation capture (Hi-C), revolutionizing the field of 3D genome biology.

    • Magda Bienko

  • Review Article |

    The ability to map DNA and RNA modifications has improved our understanding of these marks, but in some cases inconsistent results have been problematic. Here, Kong et al. discuss how to recognize and resolve issues associated with commonly used sequencing-based approaches to minimize mapping errors.

    • Yimeng Kong
    • , Edward A. Mead
    •  & Gang Fang

  • Review Article |

    In this Review, Spitale and Incarnato discuss how the application of sequencing-based RNA structure mapping methods to entire transcriptomes in living cells is providing insight into the RNA structurome, the dynamics of RNA ensembles and how RNA structure regulates cellular processes.

    • Robert C. Spitale
    •  & Danny Incarnato

  • Research Highlight |

    A paper in Cancer Cell reports genetic ancestry-associated differences in clinical outcomes when using tumour mutational burden as a biomarker in the context of immune checkpoint inhibitor therapy.

    • Linda Koch

  • Research Highlight |

    A study in Nature describes ‘DNA Typewriter’, a prime-editing-based DNA recording technology that can capture the order of large numbers of distinct molecular events in mammalian cells.

    • Kirsty Minton

  • Research Highlight |

    Two recent studies report microbial genome and gene catalogues that archive oceanic and glacial genomic and functional diversity at scale and yield insights into their biosynthetic potential.

    • Linda Koch

  • Research Highlight |

    A report in Cell takes single-cell CRISPR screens to genome scale and demonstrates how the transcriptional phenotypes can be used to resolve gene functions.

    • Lucia Brunello

  • Research Highlight |

    Gegenhuber et al. now show that, in mice, a neonatal surge in oestradiol activates oestrogen receptor-α to drive a sustained male-typical gene expression programme that determines brain sexual differentiation.

    • Katharine H. Wrighton

  • Review Article |

    Publicly available sequencing data can be used as external common controls for rare variant analyses but cautious sample ascertainment and processing is needed to avoid bias and confounding. The authors review opportunities and challenges for the robust use of common controls in genetic studies, including study design, infrastructure and quality control considerations.

    • Genevieve L. Wojcik
    • , Jessica Murphy
    •  & Audrey E. Hendricks

  • Journal Club |

    Lillian Musila highlights a paper by Quick et al., which reported the use of portable nanopore sequencing for on-site, real-time genomic surveillance during the 2014–2016 Ebola virus epidemic.

    • Lillian Musila

  • Research Highlight |

    In six new studies published in Science, the Telomere-to-Telomere (T2T) Consortium reports the assembly and initial characterization of the final, previously unresolved 8% of the human genome.

    • Michael Attwaters

  • In Brief |

    A paper in Molecular Cell reports EpiDamID, a new tool for simultaneously profiling transcription and histone post-translation modifications in single cells.

    • Dorothy Clyde

  • In Brief |

    A paper in Nature Biotechnology describes epigenetic expression inference from cfDNA-sequencing (EPIC-seq), and demonstrates its use for non-invasive classification of cancers.

    • Dorothy Clyde

  • Review Article |

    Single-cell transcriptomics is beginning to systematically define commonalities but also heterogeneity within and between organs for multiple human cell types. Here, the authors review emerging biological insights from cross-tissue single-cell transcriptomic studies into epithelial, fibroblast, vascular and immune cells.

    • Rasa Elmentaite
    • , Cecilia Domínguez Conde
    •  & Sarah A. Teichmann

  • Review Article |

    In this Review, Ding, Sharon and Bar-Joseph discuss how dynamic features can be incorporated into single-cell transcriptomics studies, using both experimental and computational strategies to provide biological insights.

    • Jun Ding
    • , Nadav Sharon
    •  & Ziv Bar-Joseph

  • Perspective |

    This Perspective highlights privacy issues related to the sharing of functional genomics data, including genotype and phenotype information leakage from different functional genomics data types and their summarization steps. The authors also review the techniques that will enable broad sharing and analysis while maintaining privacy.

    • Gamze Gürsoy
    • , Tianxiao Li
    •  & Mark B. Gerstein

  • Research Highlight |

    Attempts to understand the role of aneuploidy in tumorigenesis have been hampered by conflicting results. Now, two new mouse models described in Genes and Development provide evidence that chromosome instability-induced aneuploidy drives T cell lymphomagenesis.

    • Dorothy Clyde

  • In Brief |

    A new method called CIM-seq analyses pairwise co-occurrences of cell types across multiplets to identify cells that are in physical contact with each other in intact tissues.

    • Linda Koch

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