Cover photo by Kevin Lim and Cedric Ng: Durio zibethinus

Durian genome

Latest Research

  • Letter |

    This study presents a probabilistic framework for inferring negative and positive selection in human cancers that addresses the problem of mutation rate variation. Applying the model to sequencing data from 17 cancer types identifies new significantly mutated genes and detects significant signals of negative selection in many cancer types.

    • Donate Weghorn
    •  & Shamil Sunyaev
  • Analysis |

    This analysis of cancer sequencing data identifies a reduced somatic mutation rate in exons and shows that this phenomenon is due to higher mismatch-repair activity in exons as compared to introns. These findings have implications for the understanding of mutational and DNA repair processes and for studying the evolution of both tumors and species.

    • Joan Frigola
    • , Radhakrishnan Sabarinathan
    • , Loris Mularoni
    • , Ferran Muiños
    • , Abel Gonzalez-Perez
    •  & Núria López-Bigas
  • 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
  • Article |

    RNA Capture Long Seq (CLS) is a new method for transcript annotation that combines targeted RNA capture with long-read sequencing. CLS reannotates GENCODE lncRNAs and increases the number of validated splice junctions and transcript models for targeted loci.

    • Julien Lagarde
    • , Barbara Uszczynska-Ratajczak
    • , Silvia Carbonell
    • , Sílvia Pérez-Lluch
    • , Amaya Abad
    • , Carrie Davis
    • , Thomas R Gingeras
    • , Adam Frankish
    • , Jennifer Harrow
    • , Roderic Guigo
    •  & Rory Johnson
  • Letter |

    This large-scale genome-wide association analysis of subjects with asthma, hay fever or eczema provides insights into the shared genetic basis of these allergic diseases. The findings suggest that these diseases partly co-occur because they share many genetic risk variants that dysregulate the expression of immune-related genes.

    • Manuel A Ferreira
    • , Judith M Vonk
    • , Hansjörg Baurecht
    • , Ingo Marenholz
    • , Chao Tian
    • , Joshua D Hoffman
    • , Quinta Helmer
    • , Annika Tillander
    • , Vilhelmina Ullemar
    • , Jenny van Dongen
    • , Yi Lu
    • , Franz Rüschendorf
    • , Jorge Esparza-Gordillo
    • , Chris W Medway
    • , Edward Mountjoy
    • , Kimberley Burrows
    • , Oliver Hummel
    • , Sarah Grosche
    • , Ben M Brumpton
    • , John S Witte
    • , Jouke-Jan Hottenga
    • , Gonneke Willemsen
    • , Jie Zheng
    • , Elke Rodríguez
    • , Melanie Hotze
    • , Andre Franke
    • , Joana A Revez
    • , Jonathan Beesley
    • , Melanie C Matheson
    • , Shyamali C Dharmage
    • , Lisa M Bain
    • , Lars G Fritsche
    • , Maiken E Gabrielsen
    • , Brunilda Balliu
    • , 23andMe Research Team
    • , AAGC collaborators
    • , BIOS consortium
    • , LifeLines Cohort Study
    • , Jonas B Nielsen
    • , Wei Zhou
    • , Kristian Hveem
    • , Arnulf Langhammer
    • , Oddgeir L Holmen
    • , Mari Løset
    • , Gonçalo R Abecasis
    • , Cristen J Willer
    • , Andreas Arnold
    • , Georg Homuth
    • , Carsten O Schmidt
    • , Philip J Thompson
    • , Nicholas G Martin
    • , David L Duffy
    • , Natalija Novak
    • , Holger Schulz
    • , Stefan Karrasch
    • , Christian Gieger
    • , Konstantin Strauch
    • , Ronald B Melles
    • , David A Hinds
    • , Norbert Hübner
    • , Stephan Weidinger
    • , Patrik K E Magnusson
    • , Rick Jansen
    • , Eric Jorgenson
    • , Young-Ae Lee
    • , Dorret I Boomsma
    • , Catarina Almqvist
    • , Robert Karlsson
    • , Gerard H Koppelman
    •  & Lavinia Paternoster
  • Article |

    Analysis of whole-genome sequencing data from 163 vervet monkeys from Africa and the Caribbean shows high diversity among taxa and identifies signatures of selection. Selection signals affect viral processes, and genes that show response to SIV in vervets but not macaques have elevated selection scores.

    • Hannes Svardal
    • , Anna J Jasinska
    • , Cristian Apetrei
    • , Giovanni Coppola
    • , Yu Huang
    • , Christopher A Schmitt
    • , Beatrice Jacquelin
    • , Vasily Ramensky
    • , Michaela Müller-Trutwin
    • , Martin Antonio
    • , George Weinstock
    • , J Paul Grobler
    • , Ken Dewar
    • , Richard K Wilson
    • , Trudy R Turner
    • , Wesley C Warren
    • , Nelson B Freimer
    •  & Magnus Nordborg

News & Comment

  • 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.

  • Commentary |

    • Jennifer A Brody
    • , Alanna C Morrison
    • , Joshua C Bis
    • , Jeffrey R O'Connell
    • , Michael R Brown
    • , Jennifer E Huffman
    • , Darren C Ames
    • , Andrew Carroll
    • , Matthew P Conomos
    • , Stacey Gabriel
    • , Richard A Gibbs
    • , Stephanie M Gogarten
    • , Namrata Gupta
    • , Cashell E Jaquish
    • , Andrew D Johnson
    • , Joshua P Lewis
    • , Xiaoming Liu
    • , Alisa K Manning
    • , George J Papanicolaou
    • , Achilleas N Pitsillides
    • , Kenneth M Rice
    • , William Salerno
    • , Colleen M Sitlani
    • , Nicholas L Smith
    • , NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
    • , The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium
    • , TOPMed Hematology and Hemostasis Working Group
    • , CHARGE Analysis and Bioinformatics Working Group
    • , Susan R Heckbert
    • , Cathy C Laurie
    • , Braxton D Mitchell
    • , Ramachandran S Vasan
    • , Stephen S Rich
    • , Jerome I Rotter
    • , James G Wilson
    • , Eric Boerwinkle
    • , Bruce M Psaty
    •  & L Adrienne Cupples
  • News and Views |

    High-resolution maps of enhancer–promoter interactions in rare primary human T cell subsets and coronary artery smooth muscle cells link variants associated with autoimmune and cardiovascular diseases to target genes. This represents an important step forward for mapping genes involved in complex diseases.

    • Gosia Trynka
  • Commentary |

    Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variant's cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.

    • eGTEx Project
    • , Barbara E Stranger
    • , Lori E Brigham
    • , Richard Hasz
    • , Marcus Hunter
    • , Christopher Johns
    • , Mark Johnson
    • , Gene Kopen
    • , William F Leinweber
    • , John T Lonsdale
    • , Alisa McDonald
    • , Bernadette Mestichelli
    • , Kevin Myer
    • , Brian Roe
    • , Michael Salvatore
    • , Saboor Shad
    • , Jeffrey A Thomas
    • , Gary Walters
    • , Michael Washington
    • , Joseph Wheeler
    • , Jason Bridge
    • , Barbara A Foster
    • , Bryan M Gillard
    • , Ellen Karasik
    • , Rachna Kumar
    • , Mark Miklos
    • , Michael T Moser
    • , Scott D Jewell
    • , Robert G Montroy
    • , Daniel C Rohrer
    • , Dana R Valley
    • , David A Davis
    • , Deborah C Mash
    • , Sarah E Gould
    • , Ping Guan
    • , Susan Koester
    • , A Roger Little
    • , Casey Martin
    • , Helen M Moore
    • , Abhi Rao
    • , Jeffery P Struewing
    • , Simona Volpi
    • , Kasper D Hansen
    • , Peter F Hickey
    • , Lindsay F Rizzardi
    • , Lei Hou
    • , Yaping Liu
    • , Benoit Molinie
    • , Yongjin Park
    • , Nicola Rinaldi
    • , Li Wang
    • , Nicholas Van Wittenberghe
    • , Melina Claussnitzer
    • , Ellen T Gelfand
    • , Qin Li
    • , Sandra Linder
    • , Rui Zhang
    • , Kevin S Smith
    • , Emily K Tsang
    • , Lin S Chen
    • , Kathryn Demanelis
    • , Jennifer A Doherty
    • , Farzana Jasmine
    • , Muhammad G Kibriya
    • , Lihua Jiang
    • , Shin Lin
    • , Meng Wang
    • , Ruiqi Jian
    • , Xiao Li
    • , Joanne Chan
    • , Daniel Bates
    • , Morgan Diegel
    • , Jessica Halow
    • , Eric Haugen
    • , Audra Johnson
    • , Rajinder Kaul
    • , Kristen Lee
    • , Matthew T Maurano
    • , Jemma Nelson
    • , Fidencio J Neri
    • , Richard Sandstrom
    • , Marian S Fernando
    • , Caroline Linke
    • , Meritxell Oliva
    • , Andrew Skol
    • , Fan Wu
    • , Joshua M Akey
    • , Andrew P Feinberg
    • , Jin Billy Li
    • , Brandon L Pierce
    • , John A Stamatoyannopoulos
    • , Hua Tang
    • , Kristin G Ardlie
    • , Manolis Kellis
    • , Michael P Snyder
    •  & Stephen B Montgomery
  • News and Views |

    Regulation of epigenetic factors through their recruitment to specific genomic regions is still poorly understood. A recent study demonstrates a global mechanism of tethering Polycomb group (PcG) proteins through sequence-specific DNA-binding factors.

    • Eduardo March
    •  & Sara Farrona

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