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  1. Finding useful data across multiple biomedical data repositories using DataMed

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    The value of broadening searches for data across multiple repositories has been identified by the biomedical research community. As part of the US National Institutes of Health (NIH) Big Data to Knowledge initiative, we work with an international community of researchers, service providers and knowledge experts to develop and test a data index and search engine, which are based on metadata extracted from various data sets in a range of repositories. DataMed is designed to be, for data, what PubMed has been for the scientific literature. DataMed supports the findability and accessibility of data sets. These characteristics—along with interoperability and reusability—compose the four FAIR principles to facilitate knowledge discovery in today's big data–intensive science landscape.

  2. Remembrance of epigenomes past

    Understanding of how epigenetic information is acquired, processed and transmitted through cell division, and potentially across generations, remains limited. Mechanistic studies aiming to elucidate the molecular underpinnings of these phenomena may provide insights into development, disease susceptibility and evolution.
  3. Adenine N6-methylation in diverse fungi

    A DNA modification—methylation of cytosines and adenines—has important roles in diverse processes such as regulation of gene expression and genome stability, yet until recently adenine methylation had been considered to be only a hallmark of prokaryotes. A new study identifies abundant adenine methylation of transcriptionally active genes in early-diverging fungi that, together with recent other work, emphasizes the importance of adenine methylation in eukaryotes.

    See also: Letter by Stephen J Mondo et al.

  4. The future of human genome editing

    With the advent of precision genome editing, the ability to modify living organisms has proceeded with remarkable speed and breadth. Any application of this technology to the human germ line must be tightly coupled to deliberate consideration of the consequences, both scientific and social, of introducing heritable alterations to the human population. We recommend constant oversight and evaluation of human germline genome editing to balance prudence with discovery, and risk with progress.
  5. Becoming weeds

    A new resequencing analysis of weedy rice (Oryza sativa L.) biotypes illuminates distinct evolutionary paths and outcomes of de-domestication and ferality. This largest effort to date in weedy plant genomics gives a better understanding of weediness while also providing a promising source of alleles for rice breeding.

    See also: Letter by Lin-Feng Li et al.

  6. A SMARCD2-containing mSWI/SNF complex is required for granulopoiesis

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    Mammalian SWI/SNF complexes have critical roles in development and differentiation, and are implicated in the pathogenesis of several diseases; however, the mechanisms underpinning disease manifestation and the specificity of the subunits mutated are incompletely understood. Newly identified loss-of-function mutations in the SMARCD2 gene (part of the SMARCD1, SMARCD2 and SMARCD3 paralog family) reveal an evolutionarily conserved role specifically for the SMARCD2 subunit in granulopoiesis, and further investigation implicates the CEBPɛ transcription factor as a key effector of this specific function.

    See also: Article by Maximilian Witzel et al., Article by Pierre Priam et al.

  7. Innate and adaptive immunity shape circulating HCV strains

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    An unbiased genome-to-genome analysis in chronic hepatitis C virus (HCV) infection confirms the innate and adaptive arms of the immune system as drivers of viral evolution. Viral adaptation has a critical role in the interaction between host and pathogen and has important clinical implications for infection outcome.

    See also: Article by M Azim Ansari et al.

  8. 25 more years

    This month, to celebrate a quarter century of excellence in genetics, we are highlighting selections from the past work we have published. We will then publish a number of forward-looking Perspectives in the coming months to examine and chart the future directions of our field. In parallel, we will also consult researchers for their answers to current questions of interest to the genetics and genomics community for discussion throughout the year.

  9. A golden goat genome

    The newly described de novo goat genome sequence is the most contiguous diploid vertebrate assembly generated thus far using whole-genome assembly and scaffolding methods. The contiguity of this assembly is approaching that of the finished human and mouse genomes and suggests an affordable roadmap to high-quality references for thousands of species.

    See also: Technical Report by Derek M Bickhart et al.

  10. Resequencing at scale in neurodevelopmental disorders

    An international collaboration has assembled DNA samples and detailed phenotypic information from >13,000 individuals with a clinical diagnosis of either autism spectrum disorder (ASD) or intellectual disability/developmental delay (ID/DD). The application of molecular inversion probe technologies to sequence 208 candidate genes at scale in this impressive resource has identified a large set of plausibly causative mutations for these disorders.

    See also: Article by Holly A F Stessman et al.

  11. The creativity of immigrants

    Countries that have benefitted from immigration to dominate the scientific research landscape cannot expect to maintain their lead after they close their borders. Nations aspiring to lead in the knowledge economy must not only be open, but also need to respect freedom of communication and free expression of ideas.

  12. The road to precision oncology

    The ultimate goal of precision medicine is to use population-based molecular, clinical and other data to make individually tailored clinical decisions for patients, although the path to achieving this goal is not entirely clear. A new study shows how knowledge banks of patient data can be used to make individual treatment decisions in acute myeloid leukemia.

    See also: Analysis by Moritz Gerstung et al.

  13. Convergence and divergence in sex-chromosome evolution

    A sequence assembly of the chicken W chromosome enables reconstruction of the gene content of the W chromosome across 14 bird species and shows striking similarities in the maintenance of broadly expressed and dosage-sensitive genes on highly degenerate sex chromosomes in both birds and mammals. However, the chicken W chromosome is not enriched for genes with expression in female-specific tissues, providing an intriguing contrast to the acquisition and amplification of genes with testis-specific expression on mammalian Y chromosomes and suggesting that the inheritance of chromosomes solely through females or males can lead to different evolutionary outcomes.

    See also: Article by Daniel W Bellott et al.

  14. Untangling the genetics from the epigenetics in pancreatic cancer metastasis

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    Comparative genomic analyses of primary tumors and metastases within individuals with pancreatic cancer have exposed the complex clonal dynamics that underlie the dissemination of cancer cells to distant sites. Recent studies implicate non-genetic mechanisms in this process, particularly fluctuations in chromatin states and metabolism, which can endow rare cells within a primary tumor with metastatic potential.

    See also: Article by Alvin P Makohon-Moore et al., Article by Oliver G McDonald et al.

  15. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer Open

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    CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants of all types. CIViC is committed to open-source code, open-access content, public application programming interfaces (APIs) and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine.

  16. It's all druggable

    Current medicines are small chemicals that target the activity of proteins in the body, resulting in therapeutic and off-target changes in metabolism and gene expression. Now, however, gene expression levels can be raised or lowered at almost any point in the genome by sequence-targeted therapeutics, and the effects of these agents can be tested in preclinical models generated by gene editing of experimental animals and human cells. Genome-wide association studies (GWAS) of disease predisposition, metabolism and gene expression have a key role in explaining how current protein-targeting drugs work and in using the regulatory variation in human genomes to guide the therapeutic future of targeted gene regulation.

  17. Many faces of SMCHD1

    The chromatin scaffolding protein SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) was previously shown to have diverse roles in X-chromosome inactivation, imprinting and double-strand break repair, and mutations in SMCHD1 contribute to a type of muscular dystrophy. Now, development of the nose and eyes is added to its list of functions.

    See also: Article by Natalie D Shaw et al., Letter by Christopher T Gordon et al.

  18. SWI/SNF complex in cancer

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    Four studies in this issue report new mechanisms underlying the function of the chromatin remodeling SWI/SNF complex in controlling gene expression and suppressing tumor development, providing valuable insights into the treatment of cancers harboring mutations in genes encoding SWI/SNF complex subunits.

    See also: Article by Cigall Kadoch et al., Letter by Benjamin Z Stanton et al., Letter by Xiaofeng Wang et al., Letter by Radhika Mathur et al.

  19. Finally accepting plant domestication

    Agriculture has depended since its Neolithic origins upon spontaneous or induced genetic variation. Human selection on naturally occurring variation in flowering is the most frequent source of domesticated crop plants. In the current era of rapid technological advance in reading and writing genomes, we advocate universal access to some safe modular variation in flower, leaf and color traits that can be operated without labs or restrictions by ordinary farmers and gardeners.