GTExTiles by Erin Dewalt

eGTEx Project

Latest Research

  • Technical Report |

    LeafCutter is a new tool that identifies variable intron splicing events from RNA-seq data for analysis of complex alternative splicing. The method does not require transcript annotation and can be used to map splicing quantitative trait loci.

    • Yang I. Li
    • , David A. Knowles
    • , Jack Humphrey
    • , Alvaro N. Barbeira
    • , Scott P. Dickinson
    • , Hae Kyung Im
    •  & Jonathan K. Pritchard
  • Article |

    This study identifies regulatory variants in sensory neurons derived from induced pluripotent stem cells. Despite differentiation-induced variability, an allele-specific method allowed detection of loci influencing gene expression, chromatin accessibility and RNA splicing.

    • Jeremy Schwartzentruber
    • , Stefanie Foskolou
    • , Helena Kilpinen
    • , Julia Rodrigues
    • , Kaur Alasoo
    • , Andrew J. Knights
    • , Minal Patel
    • , Angela Goncalves
    • , Rita Ferreira
    • , Caroline Louise Benn
    • , Anna Wilbrey
    • , Magda Bictash
    • , Emma Impey
    • , Lishuang Cao
    • , Sergio Lainez
    • , Alexandre Julien Loucif
    • , Paul John Whiting
    • , Alex Gutteridge
    •  & Daniel J. Gaffney
  • Article |

    TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit bivalent promoter hypermethylation without a corresponding decrease in gene expression in the undifferentiated state. However, PAX6 promoter hypermethylation in TKO hESCs impairs neural differentiation.

    • Nipun Verma
    • , Heng Pan
    • , Louis C. Doré
    • , Abhijit Shukla
    • , Qing V. Li
    • , Bobbie Pelham-Webb
    • , Virginia Teijeiro
    • , Federico González
    • , Andrei Krivtsov
    • , Chan-Jung Chang
    • , Eirini P. Papapetrou
    • , Chuan He
    • , Olivier Elemento
    •  & Danwei Huangfu
  • Article |

    Transcriptome, DNA methylome and Hi-C profiling of peri- and post-implantation mouse cell lineages identified allele- and lineage-specific methylation patterns. Global demethylation and remethylation correlate with megabase chromatin compartments.

    • Yu Zhang
    • , Yunlong Xiang
    • , Qiangzong Yin
    • , Zhenhai Du
    • , Xu Peng
    • , Qiujun Wang
    • , Miguel Fidalgo
    • , Weikun Xia
    • , Yuanyuan Li
    • , Zhen-ao Zhao
    • , Wenhao Zhang
    • , Jing Ma
    • , Feng Xu
    • , Jianlong Wang
    • , Lei Li
    •  & Wei Xie
  • Article |

    This study uses human astrocytes and glioma tumorspheres to generate an atlas of mutant-IDH1-induced epigenomic reprogramming. The findings have implications for understanding mutant IDH function and for optimizing approaches to target IDH-mutant tumors.

    • Sevin Turcan
    • , Vladimir Makarov
    • , Julian Taranda
    • , Yuxiang Wang
    • , Armida W. M. Fabius
    • , Wei Wu
    • , Yupeng Zheng
    • , Nour El-Amine
    • , Sara Haddock
    • , Gouri Nanjangud
    • , H. Carl LeKaye
    • , Cameron Brennan
    • , Justin Cross
    • , Jason T. Huse
    • , Neil L. Kelleher
    • , Pavel Osten
    • , Craig B. Thompson
    •  & Timothy A. Chan
  • Article |

    Analysis of a large cohort of EGFR-mutant lung cancer cell-free DNA samples along with longitudinal samples from a patient with EGFR-mutant lung cancer identifies pathways that inhibit EGFR-inhibitor response. Co-occurring genetic alterations influence clinical outcomes and underscore the need for combination therapies.

    • Collin M Blakely
    • , Thomas B K Watkins
    • , Wei Wu
    • , Beatrice Gini
    • , Jacob J Chabon
    • , Caroline E McCoach
    • , Nicholas McGranahan
    • , Gareth A Wilson
    • , Nicolai J Birkbak
    • , Victor R Olivas
    • , Julia Rotow
    • , Ashley Maynard
    • , Victoria Wang
    • , Matthew A Gubens
    • , Kimberly C Banks
    • , Richard B Lanman
    • , Aleah F Caulin
    • , John St John
    • , Anibal R Cordero
    • , Petros Giannikopoulos
    • , Andrew D Simmons
    • , Philip C Mack
    • , David R Gandara
    • , Hatim Husain
    • , Robert C Doebele
    • , Jonathan W Riess
    • , Maximilian Diehn
    • , Charles Swanton
    •  & Trever G Bivona

News & Comment

  • News and Views |

    A new study reports genome-wide variation in 163 vervet monkeys from across their taxonomic and geographic ranges. The analysis suggests a complex history of admixture and identifies signals of repeated evolutionary selection, some of which may be linked to response to simian immunodeficiency virus.

    • Ellen M Leffler
  • News and Views |

    The CRISPR–Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high copy number. A new study describes a computational approach to correct for this copy number effect, increasing the specificity of CRIPSR screens to identify essential genes.

    • John Paul Shen
    •  & Trey Ideker
  • Editorial |

    In the motivation, conduct and reporting of science, there is no substitute for reason, and it must prevail whenever scientific methods are used. Similarly, scientific recommendations can only be useful if they meet with rational decision-making. Because people come to decisions from diverse viewpoints and values, listening to the values and views of scientists and non-scientists—while explicitly refraining from debate and persuasion—may point the way to determining when and where scientific ideas are of interest and likely to be adopted.

  • News and Views |

    A new analysis of cancer genomes identifies a decrease in the mutation burden of exons, but not introns, as compared to expectation. This difference can be explained by preferential recruitment of the DNA mismatch repair machinery to a protein modification that marks exons.

    • Dashiell J Massey
    •  & Amnon Koren
  • News and Views |

    Human-derived tumor models are becoming popular in the context of personalized medicine, but a new study shows that these models could be less representative of primary tumors than previously thought, particularly when using late passages.

    • Carlos Villacorta-Martin
    • , Amanda J Craig
    •  & Augusto Villanueva
  • Editorial |

    Citation of prior publications is essential both to claim that knowledge is needed in your area of research and to establish that you have indeed advanced understanding substantially in that area. The journal deplores and will decline to consider manuscripts that fail to identify the key findings of published articles and that—deliberately or inadvertently—omit the reason the prior work is cited.

For Authors

For Referees

  • This section provides information you will need when reviewing a manuscript for Nature Genetics.
  • The primary purpose of the review is to provide the editors with the information needed to reach a decision.
  • We strongly encourage referees to submit their comments via our online submission system by following the link provided in the editor’s email.
  • Reviewers are normally asked to referee all revisions of a paper, and are informed of the decisions being taken by the editors.

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