Browse Articles

  • 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
  • Article |

    The authors resequence a core collection of upland cotton (Gossypium hirsutum) comprising 419 accessions. They analyze genomic variation and conduct a genome-wide association study for 13 fiber quality and yield traits in 12 different environments.

    • Zhiying Ma
    • , Shoupu He
    • , Xingfen Wang
    • , Junling Sun
    • , Yan Zhang
    • , Guiyin Zhang
    • , Liqiang Wu
    • , Zhikun Li
    • , Zhihao Liu
    • , Gaofei Sun
    • , Yuanyuan Yan
    • , Yinhua Jia
    • , Jun Yang
    • , Zhaoe Pan
    • , Qishen Gu
    • , Xueyuan Li
    • , Zhengwen Sun
    • , Panhong Dai
    • , Zhengwen Liu
    • , Wenfang Gong
    • , Jinhua Wu
    • , Mi Wang
    • , Hengwei Liu
    • , Keyun Feng
    • , Huifeng Ke
    • , Junduo Wang
    • , Hongyu Lan
    • , Guoning Wang
    • , Jun Peng
    • , Nan Wang
    • , Liru Wang
    • , Baoyin Pang
    • , Zhen Peng
    • , Ruiqiang Li
    • , Shilin Tian
    •  & Xiongming Du
  • Letter |

    The authors report an improved genome assembly of G. arboretum and resequencing of 243 diploid cotton accessions. GWAS and QTL-seq identify a number of candidate loci that associate with seed oil content, disease resistance and yield traits in cotton.

    • Xiongming Du
    • , Gai Huang
    • , Shoupu He
    • , Zhaoen Yang
    • , Gaofei Sun
    • , Xiongfeng Ma
    • , Nan Li
    • , Xueyan Zhang
    • , Junling Sun
    • , Min Liu
    • , Yinhua Jia
    • , Zhaoe Pan
    • , Wenfang Gong
    • , Zhaohui Liu
    • , Heqin Zhu
    • , Lei Ma
    • , Fuyan Liu
    • , Daigang Yang
    • , Fan Wang
    • , Wei Fan
    • , Qian Gong
    • , Zhen Peng
    • , Liru Wang
    • , Xiaoyang Wang
    • , Shuangjiao Xu
    • , Haihong Shang
    • , Cairui Lu
    • , Hongkun Zheng
    • , Sanwen Huang
    • , Tao Lin
    • , Yuxian Zhu
    •  & Fuguang Li
  • Article |

    This study shows that UTX (KDM6A) suppresses myeloid leukemogenesis through noncatalytic functions. UTX loss leads to alterations in H3K27ac, H3K4me1 and chromatin accessibility, and in gene-regulatory programs mediated by ETS and GATA transcription factors.

    • Malgorzata Gozdecka
    • , Eshwar Meduri
    • , Milena Mazan
    • , Konstantinos Tzelepis
    • , Monika Dudek
    • , Andrew J. Knights
    • , Mercedes Pardo
    • , Lu Yu
    • , Jyoti S. Choudhary
    • , Emmanouil Metzakopian
    • , Vivek Iyer
    • , Haiyang Yun
    • , Naomi Park
    • , Ignacio Varela
    • , Ruben Bautista
    • , Grace Collord
    • , Oliver Dovey
    • , Dimitrios A. Garyfallos
    • , Etienne De Braekeleer
    • , Saki Kondo
    • , Jonathan Cooper
    • , Berthold Göttgens
    • , Lars Bullinger
    • , Paul A. Northcott
    • , David Adams
    • , George S. Vassiliou
    •  & Brian J. P. Huntly
  • Letter | | open

    High-quality genome assembly of diploid Rosa chinensis and resequencing of major genotypes highlights the origin of modern rose cultivars and provides insights into color biosynthesis and scent pathways.

    • Olivier Raymond
    • , Jérôme Gouzy
    • , Jérémy Just
    • , Hélène Badouin
    • , Marion Verdenaud
    • , Arnaud Lemainque
    • , Philippe Vergne
    • , Sandrine Moja
    • , Nathalie Choisne
    • , Caroline Pont
    • , Sébastien Carrère
    • , Jean-Claude Caissard
    • , Arnaud Couloux
    • , Ludovic Cottret
    • , Jean-Marc Aury
    • , Judit Szécsi
    • , David Latrasse
    • , Mohammed-Amin Madoui
    • , Léa François
    • , Xiaopeng Fu
    • , Shu-Hua Yang
    • , Annick Dubois
    • , Florence Piola
    • , Antoine Larrieu
    • , Magali Perez
    • , Karine Labadie
    • , Lauriane Perrier
    • , Benjamin Govetto
    • , Yoan Labrousse
    • , Priscilla Villand
    • , Claudia Bardoux
    • , Véronique Boltz
    • , Céline Lopez-Roques
    • , Pascal Heitzler
    • , Teva Vernoux
    • , Michiel Vandenbussche
    • , Hadi Quesneville
    • , Adnane Boualem
    • , Abdelhafid Bendahmane
    • , Chang Liu
    • , Manuel Le Bris
    • , Jérôme Salse
    • , Sylvie Baudino
    • , Moussa Benhamed
    • , Patrick Wincker
    •  & Mohammed Bendahmane
  • 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.

  • Analysis |

    This analysis compares methods for estimating the heritability and genetic architecture of complex traits using whole-genome data. The results provide guidance for best practices and proper interpretation of published heritability estimates.

    • Luke M. Evans
    • , Rasool Tahmasbi
    • , Scott I. Vrieze
    • , Gonçalo R. Abecasis
    • , Sayantan Das
    • , Steven Gazal
    • , Douglas W. Bjelland
    • , Teresa R. de Candia
    • , Michael E. Goddard
    • , Benjamin M. Neale
    • , Jian Yang
    • , Peter M. Visscher
    •  & Matthew C. Keller
  • Article |

    A genome-wide association meta-analysis of individuals with clinically assessed or self-reported depression identifies 44 independent risk loci. Comparisons with other psychiatric disorders and candidate gene analyses provide new insights into major depressive disorder.

    • Naomi R. Wray
    • , Stephan Ripke
    • , Manuel Mattheisen
    • , Maciej Trzaskowski
    • , Enda M. Byrne
    • , Abdel Abdellaoui
    • , Mark J. Adams
    • , Esben Agerbo
    • , Tracy M. Air
    • , Till M. F. Andlauer
    • , Silviu-Alin Bacanu
    • , Marie Bækvad-Hansen
    • , Aartjan F. T. Beekman
    • , Tim B. Bigdeli
    • , Elisabeth B. Binder
    • , Douglas R. H. Blackwood
    • , Julien Bryois
    • , Henriette N. Buttenschøn
    • , Jonas Bybjerg-Grauholm
    • , Na Cai
    • , Enrique Castelao
    • , Jane Hvarregaard Christensen
    • , Toni-Kim Clarke
    • , Jonathan I. R. Coleman
    • , Lucía Colodro-Conde
    • , Baptiste Couvy-Duchesne
    • , Nick Craddock
    • , Gregory E. Crawford
    • , Cheynna A. Crowley
    • , Hassan S. Dashti
    • , Gail Davies
    • , Ian J. Deary
    • , Franziska Degenhardt
    • , Eske M. Derks
    • , Nese Direk
    • , Conor V. Dolan
    • , Erin C. Dunn
    • , Thalia C. Eley
    • , Nicholas Eriksson
    • , Valentina Escott-Price
    • , Farnush Hassan Farhadi Kiadeh
    • , Hilary K. Finucane
    • , Andreas J. Forstner
    • , Josef Frank
    • , Héléna A. Gaspar
    • , Michael Gill
    • , Paola Giusti-Rodríguez
    • , Fernando S. Goes
    • , Scott D. Gordon
    • , Jakob Grove
    • , Lynsey S. Hall
    • , Eilis Hannon
    • , Christine Søholm Hansen
    • , Thomas F. Hansen
    • , Stefan Herms
    • , Ian B. Hickie
    • , Per Hoffmann
    • , Georg Homuth
    • , Carsten Horn
    • , Jouke-Jan Hottenga
    • , David M. Hougaard
    • , Ming Hu
    • , Craig L. Hyde
    • , Marcus Ising
    • , Rick Jansen
    • , Fulai Jin
    • , Eric Jorgenson
    • , James A. Knowles
    • , Isaac S. Kohane
    • , Julia Kraft
    • , Warren W. Kretzschmar
    • , Jesper Krogh
    • , Zoltán Kutalik
    • , Jacqueline M. Lane
    • , Yihan Li
    • , Yun Li
    • , Penelope A. Lind
    • , Xiaoxiao Liu
    • , Leina Lu
    • , Donald J. MacIntyre
    • , Dean F. MacKinnon
    • , Robert M. Maier
    • , Wolfgang Maier
    • , Jonathan Marchini
    • , Hamdi Mbarek
    • , Patrick McGrath
    • , Peter McGuffin
    • , Sarah E. Medland
    • , Divya Mehta
    • , Christel M. Middeldorp
    • , Evelin Mihailov
    • , Yuri Milaneschi
    • , Lili Milani
    • , Jonathan Mill
    • , Francis M. Mondimore
    • , Grant W. Montgomery
    • , Sara Mostafavi
    • , Niamh Mullins
    • , Matthias Nauck
    • , Bernard Ng
    • , Michel G. Nivard
    • , Dale R. Nyholt
    • , Paul F. O’Reilly
    • , Hogni Oskarsson
    • , Michael J. Owen
    • , Jodie N. Painter
    • , Carsten Bøcker Pedersen
    • , Marianne Giørtz Pedersen
    • , Roseann E. Peterson
    • , Erik Pettersson
    • , Wouter J. Peyrot
    • , Giorgio Pistis
    • , Danielle Posthuma
    • , Shaun M. Purcell
    • , Jorge A. Quiroz
    • , Per Qvist
    • , John P. Rice
    • , Brien P. Riley
    • , Margarita Rivera
    • , Saira Saeed Mirza
    • , Richa Saxena
    • , Robert Schoevers
    • , Eva C. Schulte
    • , Ling Shen
    • , Jianxin Shi
    • , Stanley I. Shyn
    • , Engilbert Sigurdsson
    • , Grant B. C. Sinnamon
    • , Johannes H. Smit
    • , Daniel J. Smith
    • , Hreinn Stefansson
    • , Stacy Steinberg
    • , Craig A. Stockmeier
    • , Fabian Streit
    • , Jana Strohmaier
    • , Katherine E. Tansey
    • , Henning Teismann
    • , Alexander Teumer
    • , Wesley Thompson
    • , Pippa A. Thomson
    • , Thorgeir E. Thorgeirsson
    • , Chao Tian
    • , Matthew Traylor
    • , Jens Treutlein
    • , Vassily Trubetskoy
    • , André G. Uitterlinden
    • , Daniel Umbricht
    • , Sandra Van der Auwera
    • , Albert M. van Hemert
    • , Alexander Viktorin
    • , Peter M. Visscher
    • , Yunpeng Wang
    • , Bradley T. Webb
    • , Shantel Marie Weinsheimer
    • , Jürgen Wellmann
    • , Gonneke Willemsen
    • , Stephanie H. Witt
    • , Yang Wu
    • , Hualin S. Xi
    • , Jian Yang
    • , Futao Zhang
    • , Volker Arolt
    • , Bernhard T. Baune
    • , Klaus Berger
    • , Dorret I. Boomsma
    • , Sven Cichon
    • , Udo Dannlowski
    • , E. C. J. de Geus
    • , J. Raymond DePaulo
    • , Enrico Domenici
    • , Katharina Domschke
    • , Tõnu Esko
    • , Hans J. Grabe
    • , Steven P. Hamilton
    • , Caroline Hayward
    • , Andrew C. Heath
    • , David A. Hinds
    • , Kenneth S. Kendler
    • , Stefan Kloiber
    • , Glyn Lewis
    • , Qingqin S. Li
    • , Susanne Lucae
    • , Pamela F. A. Madden
    • , Patrik K. Magnusson
    • , Nicholas G. Martin
    • , Andrew M. McIntosh
    • , Andres Metspalu
    • , Ole Mors
    • , Preben Bo Mortensen
    • , Bertram Müller-Myhsok
    • , Merete Nordentoft
    • , Markus M. Nöthen
    • , Michael C. O’Donovan
    • , Sara A. Paciga
    • , Nancy L. Pedersen
    • , Brenda W. J. H. Penninx
    • , Roy H. Perlis
    • , David J. Porteous
    • , James B. Potash
    • , Martin Preisig
    • , Marcella Rietschel
    • , Catherine Schaefer
    • , Thomas G. Schulze
    • , Jordan W. Smoller
    • , Kari Stefansson
    • , Henning Tiemeier
    • , Rudolf Uher
    • , Henry Völzke
    • , Myrna M. Weissman
    • , Thomas Werge
    • , Ashley R. Winslow
    • , Cathryn M. Lewis
    • , Douglas F. Levinson
    • , Gerome Breen
    • , Anders D. Børglum
    •  & Patrick F. Sullivan
  • 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
  • Analysis |

    MACHINA is an algorithm that analyzes metastatic cancer sequence data to simultaneously infer clone trees and migration histories. Analysis of different metastatic cancer datasets provides more evidence for simple, rather than complex, migration patterns.

    • Mohammed El-Kebir
    • , Gryte Satas
    •  & Benjamin J. Raphael
  • Analysis |

    This study presents a framework to evaluate rare and de novo variation from whole-genome sequencing (WGS). The work suggests that robust results from WGS studies will require large cohorts and strategies that consider the substantial multiple-testing burden.

    • Donna M. Werling
    • , Harrison Brand
    • , Joon-Yong An
    • , Matthew R. Stone
    • , Lingxue Zhu
    • , Joseph T. Glessner
    • , Ryan L. Collins
    • , Shan Dong
    • , Ryan M. Layer
    • , Eirene Markenscoff-Papadimitriou
    • , Andrew Farrell
    • , Grace B. Schwartz
    • , Harold Z. Wang
    • , Benjamin B. Currall
    • , Xuefang Zhao
    • , Jeanselle Dea
    • , Clif Duhn
    • , Carolyn A. Erdman
    • , Michael C. Gilson
    • , Rachita Yadav
    • , Robert E. Handsaker
    • , Seva Kashin
    • , Lambertus Klei
    • , Jeffrey D. Mandell
    • , Tomasz J. Nowakowski
    • , Yuwen Liu
    • , Sirisha Pochareddy
    • , Louw Smith
    • , Michael F. Walker
    • , Matthew J. Waterman
    • , Xin He
    • , Arnold R. Kriegstein
    • , John L. Rubenstein
    • , Nenad Sestan
    • , Steven A. McCarroll
    • , Benjamin M. Neale
    • , Hilary Coon
    • , A. Jeremy Willsey
    • , Joseph D. Buxbaum
    • , Mark J. Daly
    • , Matthew W. State
    • , Aaron R. Quinlan
    • , Gabor T. Marth
    • , Kathryn Roeder
    • , Bernie Devlin
    • , Michael E. Talkowski
    •  & Stephan J. Sanders
  • Article |

    Analysis of glioblastoma samples and derived neurospheres and xenografts shows that chromosomal and extrachromosomal alterations often display divergent inheritance patterns during cell culture and xenografting.

    • Ana C. deCarvalho
    • , Hoon Kim
    • , Laila M. Poisson
    • , Mary E. Winn
    • , Claudius Mueller
    • , David Cherba
    • , Julie Koeman
    • , Sahil Seth
    • , Alexei Protopopov
    • , Michelle Felicella
    • , Siyuan Zheng
    • , Asha Multani
    • , Yongying Jiang
    • , Jianhua Zhang
    • , Do-Hyun Nam
    • , Emanuel F. Petricoin
    • , Lynda Chin
    • , Tom Mikkelsen
    •  & Roel G. W. Verhaak
  • Author Correction |

    • Francesc Coll
    • , Jody Phelan
    • , Grant A. Hill-Cawthorne
    • , Mridul B. Nair
    • , Kim Mallard
    • , Shahjahan Ali
    • , Abdallah M. Abdallah
    • , Saad Alghamdi
    • , Mona Alsomali
    • , Abdallah O. Ahmed
    • , Stephanie Portelli
    • , Yaa Oppong
    • , Adriana Alves
    • , Theolis Barbosa Bessa
    • , Susana Campino
    • , Maxine Caws
    • , Anirvan Chatterjee
    • , Amelia C. Crampin
    • , Keertan Dheda
    • , Nicholas Furnham
    • , Judith R. Glynn
    • , Louis Grandjean
    • , Dang Minh Ha
    • , Rumina Hasan
    • , Zahra Hasan
    • , Martin L. Hibberd
    • , Moses Joloba
    • , Edward C. Jones-López
    • , Tomoshige Matsumoto
    • , Anabela Miranda
    • , David J. Moore
    • , Nora Mocillo
    • , Stefan Panaiotov
    • , Julian Parkhill
    • , Carlos Penha
    • , João Perdigão
    • , Isabel Portugal
    • , Zineb Rchiad
    • , Jaime Robledo
    • , Patricia Sheen
    • , Nashwa Talaat Shesha
    • , Frik A. Sirgel
    • , Christophe Sola
    • , Erivelton Oliveira Sousa
    • , Elizabeth M. Streicher
    • , Paul Van Helden
    • , Miguel Viveiros
    • , Robert M. Warren
    • , Ruth McNerney
    • , Arnab Pain
    •  & Taane G. Clark
  • Publisher Correction |

    • Jeramiah J. Smith
    • , Nataliya Timoshevskaya
    • , Chengxi Ye
    • , Carson Holt
    • , Melissa C. Keinath
    • , Hugo J. Parker
    • , Malcolm E. Cook
    • , Jon E. Hess
    • , Shawn R. Narum
    • , Francesco Lamanna
    • , Henrik Kaessmann
    • , Vladimir A. Timoshevskiy
    • , Courtney K. M. Waterbury
    • , Cody Saraceno
    • , Leanne M. Wiedemann
    • , Sofia M. C. Robb
    • , Carl Baker
    • , Evan E. Eichler
    • , Dorit Hockman
    • , Tatjana Sauka-Spengler
    • , Mark Yandell
    • , Robb Krumlauf
    • , Greg Elgar
    •  & Chris T. Amemiya