Fynbos metabolic archive of the hyrax by Ree Treweek

Expanding the toolbox for 3D genomics

Latest Research

  • Letter |

    Shortening of mRNA 3′ UTRs is often observed in cancer. A combination of model-based analysis and experiments suggests that 3′ UTR shortening disrupts competing endogenous RNA crosstalk, thus influencing tumor-suppressor expression in trans.

    • Hyun Jung Park
    • , Ping Ji
    • , Soyeon Kim
    • , Zheng Xia
    • , Benjamin Rodriguez
    • , Lei Li
    • , Jianzhong Su
    • , Kaifu Chen
    • , Chioniso P. Masamha
    • , David Baillat
    • , Camila R. Fontes-Garfias
    • , Ann-Bin Shyu
    • , Joel R. Neilson
    • , Eric J. Wagner
    •  & Wei Li
  • Article |

    VAMP-seq is a scalable assay that measures the effects of missense variants on intracellular protein abundance. Applying VAMP-seq to thousands of PTEN and TPMT variants helps to classify them as pathogenic or benign.

    • Kenneth A. Matreyek
    • , Lea M. Starita
    • , Jason J. Stephany
    • , Beth Martin
    • , Melissa A. Chiasson
    • , Vanessa E. Gray
    • , Martin Kircher
    • , Arineh Khechaduri
    • , Jennifer N. Dines
    • , Ronald J. Hause
    • , Smita Bhatia
    • , William E. Evans
    • , Mary V. Relling
    • , Wenjian Yang
    • , Jay Shendure
    •  & Douglas M. Fowler
  • Letter |

    A meta-analysis of 139,555 Europeans identifies 68 new genomic loci associated with intraocular pressure. Incorporating these new findings into genetic models improves risk prediction for primary open-angle glaucoma.

    • Anthony P. Khawaja
    • , Jessica N. Cooke Bailey
    • , Nicholas J. Wareham
    • , Robert A. Scott
    • , Mark Simcoe
    • , Robert P. Igo Jr
    • , Yeunjoo E. Song
    • , Robert Wojciechowski
    • , Ching-Yu Cheng
    • , Peng T. Khaw
    • , Louis R. Pasquale
    • , Jonathan L. Haines
    • , Paul J. Foster
    • , Janey L. Wiggs
    • , Chris J. Hammond
    •  & Pirro G. Hysi
  • Article |

    Integration of single-cell RNA sequencing with genome-wide association data implicates specific brain cell types in schizophrenia. Gene sets previously associated with schizophrenia implicate the same cell types, which include pyramidal cells and medium spiny neurons.

    • Nathan G. Skene
    • , Julien Bryois
    • , Trygve E. Bakken
    • , Gerome Breen
    • , James J. Crowley
    • , Héléna A. Gaspar
    • , Paola Giusti-Rodriguez
    • , Rebecca D. Hodge
    • , Jeremy A. Miller
    • , Ana B. Muñoz-Manchado
    • , Michael C. O’Donovan
    • , Michael J. Owen
    • , Antonio F. Pardiñas
    • , Jesper Ryge
    • , James T. R. Walters
    • , Sten Linnarsson
    • , Ed S. Lein
    • , Patrick F. Sullivan
    •  & Jens Hjerling-Leffler
  • Article |

    Genomic analysis of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients identifies the transmission dynamics of Mtb in Vietnam including frequent transmission of Beijing lineage and positive selection for EsxW Beijing variant.

    • Kathryn E. Holt
    • , Paul McAdam
    • , Phan Vuong Khac Thai
    • , Nguyen Thuy Thuong Thuong
    • , Dang Thi Minh Ha
    • , Nguyen Ngoc Lan
    • , Nguyen Huu Lan
    • , Nguyen Thi Quynh Nhu
    • , Hoang Thanh Hai
    • , Vu Thi Ngoc Ha
    • , Guy Thwaites
    • , David J. Edwards
    • , Artika P. Nath
    • , Kym Pham
    • , David B. Ascher
    • , Jeremy Farrar
    • , Chiea Chuen Khor
    • , Yik Ying Teo
    • , Michael Inouye
    • , Maxine Caws
    •  & Sarah J. Dunstan
  • Article |

    Genome-wide cross-trait analysis shows a strong genetic correlation between asthma and allergic diseases. Shared susceptibility loci are enriched for genes involved in immune and inflammatory responses and genes expressed in epithelial tissues.

    • Zhaozhong Zhu
    • , Phil H. Lee
    • , Mark D. Chaffin
    • , Wonil Chung
    • , Po-Ru Loh
    • , Quan Lu
    • , David C. Christiani
    •  & Liming Liang

News & Comment

  • News & Views |

    The ability to visualize and study the 3D folding of chromosomes in cells has been propelled forward by several major technological advances in the past two decades. Two new studies now further expand the scientific toolbox for studying chromosome conformation by providing novel methodologies for accurate mapping of genome topology and predicting the topological effects of genomic structural variation.

    • Ralph Stadhouders
  • Editorial |

    With new ways to examine the effects of mutations on gene expression within the 3D genome and increased emphasis on finding these variants by sequencing whole genomes, we would really like to know more about the rules that govern noncoding and regulatory sequences.

  • News & Views |

    The triplet code underpins analyses of rare and de novo mutations in exome sequencing data, but analysis of the noncoding genome is much more challenging. A new analytical framework for common, complex diseases highlights the need for very large samples to overcome the unavoidable multiple-testing burden and hence provides preemptive warnings against underpowered studies.

    • Naomi R. Wray
    •  & Jacob Gratten
  • Editorial |

    Largely owing to inequitable distribution of resources, the United States is failing its population in healthcare, for which it vastly overspends relative to other wealthy countries. We advocate extending research in genetic epidemiology to oversample poor people, underserved ancestry groups and ethnic minorities, as well as to use genetic predisposition as a baseline from which to examine environmental influences on the costly comorbidities of common diseases.

  • News & Views |

    In vivo verification of tumor suppressors and their interactions with each other has required complex experiments. A report in this issue uses a novel CRISPR–Cas9 technology with barcodes to test, in parallel, the tumorigenic potential of functional loss of multiple tumor-suppressor genes in the context of a genetically engineered mouse model of lung adenocarcinoma with mutant Kras.

    • James Kim
    •  & John D. Minna

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