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Volume 49 Issue 5, May 2017

Stochasticity mosaic by Andy Feinberg, after a portrait of Conrad Waddington by Ruth Collet (p 719)


  • 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.



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News & Views

  • 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.

    • C Neal Stewart Jr
    News & Views
  • 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.

    • Brittany C Michel
    • Cigall Kadoch
    News & Views
  • 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.

    • Silvana Gaudieri
    • Michaela Lucas
    News & Views
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  • Ryan Emerson and colleagues report immunosequencing of the variable region of the TCRβ chain in 666 individuals with known cytomegalovirus (CMV) status. They show that CMV status and HLA genotype shape the T cell repertoire and demonstrate proof of principle that TCRβ sequencing can be used as a specific diagnostic of pathogen exposure.

    • Ryan O Emerson
    • William S DeWitt
    • Harlan S Robins
  • Chris Spencer, Eleanor Barnes and colleagues use human genotyping arrays and whole-genome viral sequencing to perform a systematic genome-to-genome study of 542 individuals chronically infected with hepatitis C virus (HCV). They show that both HLA alleles and genes encoding factors of the innate immune system drive viral genome polymorphism and that IFNL4 genotypes determine HCV viral load through a mechanism dependent on a specific polymorphism encoded in the HCV polyprotein.

    • M Azim Ansari
    • Vincent Pedergnana
    • Chris C A Spencer
  • Paul Pharoah and colleagues report the results of a large genome-wide association study of ovarian cancer. They identify new susceptibility loci for different epithelial ovarian cancer histotypes and use integrated analyses of genes and regulatory features at each locus to predict candidate susceptibility genes, including OBFC1.

    • Catherine M Phelan
    • Karoline B Kuchenbaecker
    • Paul D P Pharoah
  • Ira Hall, Donald Conrad, the GTEx consortium and colleagues identify 23,602 high-confidence structural variants (SVs) and 24,884 cis expression quantitative trait loci (eQTLs) across 13 human tissues. They estimate that SVs are the causal variant at 3.5–6.8% of eQTLs and identify 789 SVs predicted to directly alter gene expression, most of which are noncoding variants in regulatory elements.

    • Colby Chiang
    • Alexandra J Scott
    • Ira M Hall
  • Francesco Cucca, Stephen Montgomery and colleagues identify regulatory variants that influence gene expression and splicing using whole-genome and transcriptome sequence data from 624 Sardinians. They find a high frequency of splicing and expression quantitative trait loci near genes involved in malarial resistance and multiple sclerosis.

    • Mauro Pala
    • Zachary Zappala
    • Stephen B Montgomery
  • Shyam Prabhakar, Paul Robson, Iain Beehuat Tan and colleagues characterize the cellular heterogeneity of colorectal tumors and their microenvironment on the basis of single-cell RNA–seq data analyzed with their newly developed clustering algorithm, reference component analysis (RCA). Their analyses identify two subtypes of cancer-associated fibroblasts and further divide tumors into subgroups with divergent survival probabilities.

    • Huipeng Li
    • Elise T Courtois
    • Shyam Prabhakar
  • Andrew Feinberg, John Goutsias and colleagues derive potential energy landscapes from bisulfite sequencing data and quantify DNA methylation stochasticity genome-wide using Shannon's entropy, identifying an association between entropy and chromatin structure. Their analysis highlights the information-theoretic nature of the epigenome and provides a methodology for studying its role in disease and aging.

    • Garrett Jenkinson
    • Elisabet Pujadas
    • Andrew P Feinberg
  • Juan Cadiñanos and colleagues perform an insertional mutagenesis screen with a single-copy inactivating Sleeping Beauty transposon to look for Pten-cooperating tumor suppressor genes in mice. They find novel candidate cancer genes, verify their clinical relevance in patient cohorts and functionally demonstrate their synergistic relationship to Pten in tumor suppression.

    • Jorge de la Rosa
    • Julia Weber
    • Juan Cadiñanos
  • Christoph Klein and colleagues identify loss-of-function mutations in SMARCD2 (BAF60b) that lead to neutropenia, specific granule deficiency and myelodysplasia. They show that SMARCD2 controls differentiation of myeloid–erythroid progenitor cells through interaction with CEBPɛ and that reduced SMARCD2 levels cause transcription and chromatin alterations in acute myeloid leukemia cells.

    • Maximilian Witzel
    • Daniel Petersheim
    • Christoph Klein
  • Julie Lessard and colleagues report that ATP-dependent SWI/SNF chromatin-remodeling complex subunit SMARCD2 is essential for granulocyte development. They find that Smarcd2-deficient mice fail to generate functioning neutrophils and eosinophils, and they determine that the divergent coiled-coil 1 and SWIB domains are responsible for functional specificity during granulocyte differentiation.

    • Pierre Priam
    • Veneta Krasteva
    • Julie A Lessard
  • Fanjiang Kong, Zhixi Tian, Xingliang Hou, Baohui Liu and colleagues report the cloning and functional characterization of J, the locus underlying the long-juvenile (LJ) trait that has enabled tropical cultivation of soybean. They show that J, an ortholog of Arabidopsis ELF3, downregulates the expression of E1, thereby promoting flowering under short-day conditions.

    • Sijia Lu
    • Xiaohui Zhao
    • Fanjiang Kong
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  • Michael Taylor, Marco Marra and colleagues analyze spatial tumor heterogeneity in 9 medulloblastomas, 16 high-grade gliomas and 10 renal cell carcinomas, using a combination of transcriptomic and genomic profiling of multiregional biopsies. They find that medulloblastomas have spatially homogeneous transcriptomes, whereas somatic mutations that affect genes suitable for targeted therapeutics are spatially heterogeneous.

    • A Sorana Morrissy
    • Florence M G Cavalli
    • Michael D Taylor
  • Beatrice Melin, Richard Houlston, Melissa Bondy and colleagues report results of a large-scale genome-wide association study of glioma. They identify five new risk loci for glioblastoma and eight new risk loci for non-glioblastoma tumors, highlighting distinct genetic etiologies for these two glioma subtypes.

    • Beatrice S Melin
    • Jill S Barnholtz-Sloan
    • Melissa L Bondy
  • Jacob George and colleagues examine whether the association of the IFNL3IFNL4 region with hepatic inflammation and fibrosis is mediated by IFN-λ3 or IFN-λ4. They find greater hepatic inflammation, fibrosis progression rate and hepatic infiltration of immune cells in individuals with the risk haplotype that produces IFN-λ3 but not IFN-λ4.

    • Mohammed Eslam
    • Duncan McLeod
    • Rosanna Santoro
  • Shamil Sunyaev, David Beier and colleagues report an analysis of the fitness effects of heterozygous protein-truncating variants from the Exome Aggregation Consortium. They find that high heterozygous selection coefficients are enriched in Mendelian disease-associated genes and essential mouse genes, suggesting that this coefficient can be used to prioritize candidate disease-associated genes from clinical exome-sequencing data.

    • Christopher A Cassa
    • Donate Weghorn
    • Shamil R Sunyaev
  • Kenneth Olsen, Ana Caicedo and colleagues analyze whole-genome sequences of two strains of weedy relatives of cultivated rice. They find that weedy rice strains are primarily descended from domesticated ancestors and that few genetic differences accompanied the emergence of weediness traits.

    • Lin-Feng Li
    • Ya-Ling Li
    • Kenneth M Olsen
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