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  • Defining minimal standards for data collection is key to creating interoperative, searchable genomic and clinical databases. We highlight here the 1+Million Genomes Minimal Dataset for Cancer, encompassing 140 items in 8 domains to foster the collection of cancer data, inform transnational cooperation and advance precision cancer medicine.

    • Michela Riba
    • Cinzia Sala
    • Giovanni Tonon
  • The recently launched Egyptian Genome Project aims to sequence genomic variants of 100,000 apparently healthy Egyptian adults, with around 8,000 individuals suspected to have a genetic disease, as well as 200 ancient Egyptian mummies. The project will provide the first comprehensive genomic dataset from Egypt and North Africa.

    • Mohamed A. Elmonem
    • Neveen A. Soliman
    • Khaled Amer
  • Achieving a diagnosis for Indigenous people living with a rare, often genetic, disease is crucial for equitable healthcare. The International Rare Disease Research Consortium convened a global Task Force to bridge the gap in diagnosing Indigenous rare diseases, and identify solutions to tackle the health inequity faced by Indigenous people.

    • Gareth Baynam
    • Daria Julkowska
    • Barend Christiaan Vorster
  • While the number of SARS-CoV-2 genome sequences grew to over 15 million, the Ultrafast Sample placement on Existing tRees (UShER) tool suite maintained a comprehensive phylogenetic tree in near real time. This experience, and critical performance improvements throughout the pandemic, provide valuable lessons for rapidly scaling analyses.

    • Angie Hinrichs
    • Cheng Ye
    • Russell Corbett-Detig
  • Keeping up with the latest variant-related research is vital for genomic medicine. Here we present LitVar 2.0, a significantly improved web-based system to accurately search for genetic variants in the unstructured literature. LitVar 2.0 provides a unified search of full text and supplementary data, and improved variant recognition accuracy.

    • Alexis Allot
    • Chih-Hsuan Wei
    • Zhiyong Lu
  • The Qatar Genome Program was established to interrogate the genomics and genetics of populations in the Middle East. Improving precision medicine strategies and building long-term research capacity are both key aims of the initiative.

    • Hamdi Mbarek
    • Said I. Ismail
  • It has been 25 years since the release of GATTACA, a film that tells the story of a credible near future in which society’s inequalities, formerly associated with race and class, have been replaced with new prejudices based on genetic determinism. Here we compare GATTACA’s fictional technologies with reality’s state of the art, assessing the legal protections afforded in today’s society against GATTACA’s dystopian future in which personal freedom and privacy rights are substantially curtailed by genomic innovations. We further discuss how GATTACA’s prescient forewarnings are still relevant today in light of the current trajectory of genomic science and technology.

    • Dov Greenbaum
    • Mark Gerstein
  • High-throughput experimental platforms have revolutionized the ability to profile biochemical and functional properties of biological sequences such as DNA, RNA and proteins. By collating several data modalities with customizable tracks rendered using intuitive visualizations, genome browsers enable an interactive and interpretable exploration of diverse types of genome profiling experiments and derived annotations. However, existing genome browser tracks are not well suited for intuitive visualization of high-resolution DNA sequence features such as transcription factor motifs. Typically, motif instances in regulatory DNA sequences are visualized as BED-based annotation tracks, which highlight the genomic coordinates of the motif instances but do not expose their specific sequences. Instead, a genome sequence track needs to be cross-referenced with the BED track to identify sequences of motif hits. Even so, quantitative information about the motif instances such as affinity or conservation as well as differences in base resolution from the consensus motif are not immediately apparent. This makes interpretation slow and challenging. This problem is compounded when analyzing several cellular states and/or molecular readouts (such as ATAC-seq and ChIP–seq) simultaneously, as coordinates of enriched regions (peaks) and the set of active transcription factor motifs vary across cell states.

    • Surag Nair
    • Arjun Barrett
    • Anshul Kundaje
  • Many large research initiatives have cumulatively enrolled thousands of patients with a range of complex medical issues but no clear genetic etiology. However, it is unclear how researchers, institutions and funders should manage the data and relationships with those participants who remain undiagnosed when these studies end. In this Comment, we outline the current literature relevant to post-study obligations in clinical genomics research and discuss the application of current guidelines to research with undiagnosed participants.

    • Meghan C. Halley
    • Euan A. Ashley
    • Holly K. Tabor
  • Thirty years ago, I had the privilege of launching Nature Genetics, the first spin-off journal bearing the famous Nature logo. Spurred on by the Human Genome Project, there were high hopes for the new journal and indeed the future of human genetics. But there was little expectation that we would launch a science publishing franchise of more than 30 sister journals — or be able to therapeutically rewrite the faulty genomes of patients. Here, I reflect on the humble beginnings of Nature Genetics and 30 years of progress in genetics.

    • Kevin Davies
  • Building on the fundamental discoveries of Mendel, plant genomics has had a major role in advancing the genetic improvement of crops worldwide, particularly in developed economies where the technologies are easily accessible. From cumbersome to more miniaturized high-throughput sequencing technologies, the field continues to evolve, providing vast opportunities for studying plant genomes with varying levels of complexity and potential real-life applications.

    • Carol Nkechi Ibe
  • Recent work has highlighted a lack of diversity in genomic studies. However, less attention has been given to epigenomics. Here, we show that epigenomic studies are lacking in diversity and propose several solutions to address this problem.

    • Charles E. Breeze
    • Stephan Beck
    • Nora Franceschini
  • Calls for diversity in genomics have motivated new global research collaborations across institutions with highly imbalanced resources. We describe practical lessons we have learned so far from designing multidisciplinary international research and capacity-building programs that prioritize equity in two intertwined programs — the NeuroGAP-Psychosis research study and GINGER training program — spanning institutions in Ethiopia, Kenya, South Africa, Uganda and the United States.

    • Alicia R. Martin
    • Rocky E. Stroud II
    • Lori B. Chibnik
  • To leverage the genetic diversity in Nigeria, we established the Non-Communicable Diseases Genetic Heritage Study (NCD-GHS) consortium to help produce a comprehensive catalog of human genetic variation in Nigeria and assess the burden and etiological characteristics of non-communicable diseases in 100,000 adults in Nigeria.

    • Segun Fatumo
    • Aminu Yakubu
    • Abasi Ene-Obong
  • The Cardiometabolic Disorders in African-Ancestry Populations (CARDINAL) study site is a well-powered, first-of-its-kind resource for developing, refining and validating methods for research into polygenic risk scores that accounts for local ancestry, to improve risk prediction in diverse populations.

    • Clement A. Adebamowo
    • Adebowale Adeyemo
    • Sally N. Adebamowo
  • Widespread enthusiasm about potential contributions of genome-edited crops to address climate change, food security, nutrition and health, environmental sustainability and diversification of agriculture is dampened by concerns about the associated risks. Analysis of the top seven risks of genome-edited crops finds that the scientific risks are comparable to those of accepted, past and current breeding methods, but failure to address regulatory, legal and trade framework, and the granting of social license, squanders the potential benefits.

    • Kevin V. Pixley
    • Jose B. Falck-Zepeda
    • Neal Gutterson
  • A concerning trend in genetics is the common use of the term ‘trans-ethnic’ to describe analyses that combine or compare several ancestrally diverse populations. In this commentary, we discuss how this term is inaccurate and alienating. We propose that geneticists avoid using the term trans-ethnic entirely and that researchers across disciplines reach a new consensus about the best terms to use to describe the populations we study.

    • Mireille Kamariza
    • Lorin Crawford
    • Hilary Finucane