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
  • Article |

    A meta-analysis of exome-wide association studies for blood lipid levels in East Asian populations identifies a novel coding variant. Exome array data from the Global Lipids Genetics Consortium were integrated and led to the discovery of novel and population-specific variants associated with cholesterol and triglycerides.

    • Xiangfeng Lu
    • , Gina M Peloso
    • , Dajiang J Liu
    • , Ying Wu
    • , He Zhang
    • , Wei Zhou
    • , Jun Li
    • , Clara Sze-man Tang
    • , Rajkumar Dorajoo
    • , Huaixing Li
    • , Jirong Long
    • , Xiuqing Guo
    • , Ming Xu
    • , Cassandra N Spracklen
    • , Yang Chen
    • , Xuezhen Liu
    • , Yan Zhang
    • , Chiea Chuen Khor
    • , Jianjun Liu
    • , Liang Sun
    • , Laiyuan Wang
    • , Yu-Tang Gao
    • , Yao Hu
    • , Kuai Yu
    • , Yiqin Wang
    • , Chloe Yu Yan Cheung
    • , Feijie Wang
    • , Jianfeng Huang
    • , Qiao Fan
    • , Qiuyin Cai
    • , Shufeng Chen
    • , Jinxiu Shi
    • , Xueli Yang
    • , Wanting Zhao
    • , Wayne H-H Sheu
    • , Stacey Shawn Cherny
    • , Meian He
    • , Alan B Feranil
    • , Linda S Adair
    • , Penny Gordon-Larsen
    • , Shufa Du
    • , Rohit Varma
    • , Yii-Der Ida Chen
    • , Xiao-Ou Shu
    • , Karen Siu Ling Lam
    • , Tien Yin Wong
    • , Santhi K Ganesh
    • , Zengnan Mo
    • , Kristian Hveem
    • , Lars G Fritsche
    • , Jonas Bille Nielsen
    • , Hung-fat Tse
    • , Yong Huo
    • , Ching-Yu Cheng
    • , Y Eugene Chen
    • , Wei Zheng
    • , E Shyong Tai
    • , Wei Gao
    • , Xu Lin
    • , Wei Huang
    • , Goncalo Abecasis
    • , GLGC Consortium
    • , Sekar Kathiresan
    • , Karen L Mohlke
    • , Tangchun Wu
    • , Pak Chung Sham
    • , Dongfeng Gu
    •  & Cristen J Willer
  • Letter |

    CERES is a new computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for copy number effects and variable sgRNA activity. Applying CERES to new genome-scale CRISPR–Cas9 essentiality screen data from 342 cancer cell lines and other published data sets shows that CERES decreases false-positive results and provides consistent estimates of sgRNA activity.

    • Robin M Meyers
    • , Jordan G Bryan
    • , James M McFarland
    • , Barbara A Weir
    • , Ann E Sizemore
    • , Han Xu
    • , Neekesh V Dharia
    • , Phillip G Montgomery
    • , Glenn S Cowley
    • , Sasha Pantel
    • , Amy Goodale
    • , Yenarae Lee
    • , Levi D Ali
    • , Guozhi Jiang
    • , Rakela Lubonja
    • , William F Harrington
    • , Matthew Strickland
    • , Ting Wu
    • , Derek C Hawes
    • , Victor A Zhivich
    • , Meghan R Wyatt
    • , Zohra Kalani
    • , Jaime J Chang
    • , Michael Okamoto
    • , Kimberly Stegmaier
    • , Todd R Golub
    • , Jesse S Boehm
    • , Francisca Vazquez
    • , David E Root
    • , William C Hahn
    •  & Aviad Tsherniak
  • Article |

    Nelson Freimer and colleagues analyze gene expression data from multiple tissue samples combined with genotype data from vervet monkeys to catalog expression quantitative trait loci (eQTLs). They generate a transcriptome resource analogous to the GTEx project and perform comparative and eQTL enrichment analyses for various traits.

    • Anna J Jasinska
    • , Ivette Zelaya
    • , Susan K Service
    • , Christine B Peterson
    • , Rita M Cantor
    • , Oi-Wa Choi
    • , Joseph DeYoung
    • , Eleazar Eskin
    • , Lynn A Fairbanks
    • , Scott Fears
    • , Allison E Furterer
    • , Yu S Huang
    • , Vasily Ramensky
    • , Christopher A Schmitt
    • , Hannes Svardal
    • , Matthew J Jorgensen
    • , Jay R Kaplan
    • , Diego Villar
    • , Bronwen L Aken
    • , Paul Flicek
    • , Rishi Nag
    • , Emily S Wong
    • , John Blangero
    • , Thomas D Dyer
    • , Marina Bogomolov
    • , Yoav Benjamini
    • , George M Weinstock
    • , Ken Dewar
    • , Chiara Sabatti
    • , Richard K Wilson
    • , J David Jentsch
    • , Wesley Warren
    • , Giovanni Coppola
    • , Roger P Woods
    •  & Nelson B Freimer
  • Letter |

    Exome-wide genetic analysis on >300,000 individuals identifies associations with plasma lipid traits. Loci significantly associated with cholesterol and triglycerides are examined together to determine the effects of alleles on type 2 diabetes and coronary artery disease risk.

    • Dajiang J Liu
    • , Gina M Peloso
    • , Haojie Yu
    • , Adam S Butterworth
    • , Xiao Wang
    • , Anubha Mahajan
    • , Danish Saleheen
    • , Connor Emdin
    • , Dewan Alam
    • , Alexessander Couto Alves
    • , Philippe Amouyel
    • , Emanuele Di Angelantonio
    • , Dominique Arveiler
    • , Themistocles L Assimes
    • , Paul L Auer
    • , Usman Baber
    • , Christie M Ballantyne
    • , Lia E Bang
    • , Marianne Benn
    • , Joshua C Bis
    • , Michael Boehnke
    • , Eric Boerwinkle
    • , Jette Bork-Jensen
    • , Erwin P Bottinger
    • , Ivan Brandslund
    • , Morris Brown
    • , Fabio Busonero
    • , Mark J Caulfield
    • , John C Chambers
    • , Daniel I Chasman
    • , Y Eugene Chen
    • , Yii-Der Ida Chen
    • , Rajiv Chowdhury
    • , Cramer Christensen
    • , Audrey Y Chu
    • , John M Connell
    • , Francesco Cucca
    • , L Adrienne Cupples
    • , Scott M Damrauer
    • , Gail Davies
    • , Ian J Deary
    • , George Dedoussis
    • , Joshua C Denny
    • , Anna Dominiczak
    • , Marie-Pierre Dubé
    • , Tapani Ebeling
    • , Gudny Eiriksdottir
    • , Tõnu Esko
    • , Aliki-Eleni Farmaki
    • , Mary F Feitosa
    • , Marco Ferrario
    • , Jean Ferrieres
    • , Ian Ford
    • , Myriam Fornage
    • , Paul W Franks
    • , Timothy M Frayling
    • , Ruth Frikke-Schmidt
    • , Lars G Fritsche
    • , Philippe Frossard
    • , Valentin Fuster
    • , Santhi K Ganesh
    • , Wei Gao
    • , Melissa E Garcia
    • , Christian Gieger
    • , Franco Giulianini
    • , Mark O Goodarzi
    • , Harald Grallert
    • , Niels Grarup
    • , Leif Groop
    • , Megan L Grove
    • , Vilmundur Gudnason
    • , Torben Hansen
    • , Tamara B Harris
    • , Caroline Hayward
    • , Joel N Hirschhorn
    • , Oddgeir L Holmen
    • , Jennifer Huffman
    • , Yong Huo
    • , Kristian Hveem
    • , Sehrish Jabeen
    • , Anne U Jackson
    • , Johanna Jakobsdottir
    • , Marjo-Riitta Jarvelin
    • , Gorm B Jensen
    • , Marit E Jørgensen
    • , J Wouter Jukema
    • , Johanne M Justesen
    • , Pia R Kamstrup
    • , Stavroula Kanoni
    • , Fredrik Karpe
    • , Frank Kee
    • , Amit V Khera
    • , Derek Klarin
    • , Heikki A Koistinen
    • , Jaspal S Kooner
    • , Charles Kooperberg
    • , Kari Kuulasmaa
    • , Johanna Kuusisto
    • , Markku Laakso
    • , Timo Lakka
    • , Claudia Langenberg
    • , Anne Langsted
    • , Lenore J Launer
    • , Torsten Lauritzen
    • , David C M Liewald
    • , Li An Lin
    • , Allan Linneberg
    • , Ruth J F Loos
    • , Yingchang Lu
    • , Xiangfeng Lu
    • , Reedik Mägi
    • , Anders Malarstig
    • , Ani Manichaikul
    • , Alisa K Manning
    • , Pekka Mäntyselkä
    • , Eirini Marouli
    • , Nicholas G D Masca
    • , Andrea Maschio
    • , James B Meigs
    • , Olle Melander
    • , Andres Metspalu
    • , Andrew P Morris
    • , Alanna C Morrison
    • , Antonella Mulas
    • , Martina Müller-Nurasyid
    • , Patricia B Munroe
    • , Matt J Neville
    • , Jonas B Nielsen
    • , Sune F Nielsen
    • , Børge G Nordestgaard
    • , Jose M Ordovas
    • , Roxana Mehran
    • , Christoper J O'Donnell
    • , Marju Orho-Melander
    • , Cliona M Molony
    • , Pieter Muntendam
    • , Sandosh Padmanabhan
    • , Colin N A Palmer
    • , Dorota Pasko
    • , Aniruddh P Patel
    • , Oluf Pedersen
    • , Markus Perola
    • , Annette Peters
    • , Charlotta Pisinger
    • , Giorgio Pistis
    • , Ozren Polasek
    • , Neil Poulter
    • , Bruce M Psaty
    • , Daniel J Rader
    • , Asif Rasheed
    • , Rainer Rauramaa
    • , Dermot F Reilly
    • , Alex P Reiner
    • , Frida Renström
    • , Stephen S Rich
    • , Paul M Ridker
    • , John D Rioux
    • , Neil R Robertson
    • , Dan M Roden
    • , Jerome I Rotter
    • , Igor Rudan
    • , Veikko Salomaa
    • , Nilesh J Samani
    • , Serena Sanna
    • , Naveed Sattar
    • , Ellen M Schmidt
    • , Robert A Scott
    • , Peter Sever
    • , Raquel S Sevilla
    • , Christian M Shaffer
    • , Xueling Sim
    • , Suthesh Sivapalaratnam
    • , Kerrin S Small
    • , Albert V Smith
    • , Blair H Smith
    • , Sangeetha Somayajula
    • , Lorraine Southam
    • , Timothy D Spector
    • , Elizabeth K Speliotes
    • , John M Starr
    • , Kathleen E Stirrups
    • , Nathan Stitziel
    • , Konstantin Strauch
    • , Heather M Stringham
    • , Praveen Surendran
    • , Hayato Tada
    • , Alan R Tall
    • , Hua Tang
    • , Jean-Claude Tardif
    • , Kent D Taylor
    • , Stella Trompet
    • , Philip S Tsao
    • , Jaakko Tuomilehto
    • , Anne Tybjaerg-Hansen
    • , Natalie R van Zuydam
    • , Anette Varbo
    • , Tibor V Varga
    • , Jarmo Virtamo
    • , Melanie Waldenberger
    • , Nan Wang
    • , Nick J Wareham
    • , Helen R Warren
    • , Peter E Weeke
    • , Joshua Weinstock
    • , Jennifer Wessel
    • , James G Wilson
    • , Peter W F Wilson
    • , Ming Xu
    • , Hanieh Yaghootkar
    • , Robin Young
    • , Eleftheria Zeggini
    • , He Zhang
    • , Neil S Zheng
    • , Weihua Zhang
    • , Yan Zhang
    • , Wei Zhou
    • , Yanhua Zhou
    • , Magdalena Zoledziewska
    • , Charge Diabetes Working Group
    • , The EPIC-InterAct Consortium
    • , EPIC-CVD Consortium
    • , GOLD Consortium
    • , VA Million Veteran Program
    • , Joanna M M Howson
    • , John Danesh
    • , Mark I McCarthy
    • , Chad A Cowan
    • , Goncalo Abecasis
    • , Panos Deloukas
    • , Kiran Musunuru
    • , Cristen J Willer
    •  & Sekar Kathiresan
  • Corrigendum |

    • Chi A Ma
    • , Jeffrey R Stinson
    • , Yuan Zhang
    • , Jordan K Abbott
    • , Michael A Weinreich
    • , Pia J Hauk
    • , Paul R Reynolds
    • , Jonathan J Lyons
    • , Celeste G Nelson
    • , Elisa Ruffo
    • , Batsukh Dorjbal
    • , Salomé Glauzy
    • , Natsuko Yamakawa
    • , Swadhinya Arjunaraja
    • , Kelsey Voss
    • , Jennifer Stoddard
    • , Julie Niemela
    • , Yu Zhang
    • , Sergio D Rosenzweig
    • , Joshua J McElwee
    • , Thomas DiMaggio
    • , Helen F Matthews
    • , Nina Jones
    • , Kelly D Stone
    • , Alejandro Palma
    • , Matías Oleastro
    • , Emma Prieto
    • , Andrea R Bernasconi
    • , Geronimo Dubra
    • , Silvia Danielian
    • , Jonathan Zaiat
    • , Marcelo A Marti
    • , Brian Kim
    • , Megan A Cooper
    • , Neil D Romberg
    • , Eric Meffre
    • , Erwin W Gelfand
    • , Andrew L Snow
    •  & Joshua D Milner
  • Corrigendum |

    • Dominik Glodzik
    • , Sandro Morganella
    • , Helen Davies
    • , Peter T Simpson
    • , Yilong Li
    • , Xueqing Zou
    • , Javier Diez-Perez
    • , Johan Staaf
    • , Ludmil B Alexandrov
    • , Marcel Smid
    • , Arie B Brinkman
    • , Inga Hansine Rye
    • , Hege Russnes
    • , Keiran Raine
    • , Colin A Purdie
    • , Sunil R Lakhani
    • , Alastair M Thompson
    • , Ewan Birney
    • , Hendrik G Stunnenberg
    • , Marc J van de Vijver
    • , John W M Martens
    • , Anne-Lise Børresen-Dale
    • , Andrea L Richardson
    • , Gu Kong
    • , Alain Viari
    • , Douglas Easton
    • , Gerard Evan
    • , Peter J Campbell
    • , Michael R Stratton
    •  & Serena Nik-Zainal
  • Erratum |

    • David Brocks
    • , Christopher R Schmidt
    • , Michael Daskalakis
    • , Hyo Sik Jang
    • , Nakul M Shah
    • , Daofeng Li
    • , Jing Li
    • , Bo Zhang
    • , Yiran Hou
    • , Sara Laudato
    • , Daniel B Lipka
    • , Johanna Schott
    • , Holger Bierhoff
    • , Yassen Assenov
    • , Monika Helf
    • , Alzbeta Ressnerova
    • , Md Saiful Islam
    • , Anders M Lindroth
    • , Simon Haas
    • , Marieke Essers
    • , Charles D Imbusch
    • , Benedikt Brors
    • , Ina Oehme
    • , Olaf Witt
    • , Michael Lübbert
    • , Jan-Philipp Mallm
    • , Karsten Rippe
    • , Rainer Will
    • , Dieter Weichenhan
    • , Georg Stoecklin
    • , Clarissa Gerhäuser
    • , Christopher C Oakes
    • , Ting Wang
    •  & Christoph Plass
  • Letter |

    Roger Milne and colleagues conduct a genome-wide association study for estrogen receptor (ER)-negative breast cancer combined with BRCA1 mutation carriers in a large cohort. They identify ten new risk variants and find high genetic correlation between breast cancer risk for BRCA1 mutation carriers and risk of ER-negative breast cancer in the general population.

    • Roger L Milne
    • , Karoline B Kuchenbaecker
    • , Kyriaki Michailidou
    • , Jonathan Beesley
    • , Siddhartha Kar
    • , Sara Lindström
    • , Shirley Hui
    • , Audrey Lemaçon
    • , Penny Soucy
    • , Joe Dennis
    • , Xia Jiang
    • , Asha Rostamianfar
    • , Hilary Finucane
    • , Manjeet K Bolla
    • , Lesley McGuffog
    • , Qin Wang
    • , Cora M Aalfs
    • , ABCTB Investigators
    • , Marcia Adams
    • , Julian Adlard
    • , Simona Agata
    • , Shahana Ahmed
    • , Habibul Ahsan
    • , Kristiina Aittomäki
    • , Fares Al-Ejeh
    • , Jamie Allen
    • , Christine B Ambrosone
    • , Christopher I Amos
    • , Irene L Andrulis
    • , Hoda Anton-Culver
    • , Natalia N Antonenkova
    • , Volker Arndt
    • , Norbert Arnold
    • , Kristan J Aronson
    • , Bernd Auber
    • , Paul L Auer
    • , Margreet G E M Ausems
    • , Jacopo Azzollini
    • , François Bacot
    • , Judith Balmaña
    • , Monica Barile
    • , Laure Barjhoux
    • , Rosa B Barkardottir
    • , Myrto Barrdahl
    • , Daniel Barnes
    • , Daniel Barrowdale
    • , Caroline Baynes
    • , Matthias W Beckmann
    • , Javier Benitez
    • , Marina Bermisheva
    • , Leslie Bernstein
    • , Yves-Jean Bignon
    • , Kathleen R Blazer
    • , Marinus J Blok
    • , Carl Blomqvist
    • , William Blot
    • , Kristie Bobolis
    • , Bram Boeckx
    • , Natalia V Bogdanova
    • , Anders Bojesen
    • , Stig E Bojesen
    • , Bernardo Bonanni
    • , Anne-Lise Børresen-Dale
    • , Aniko Bozsik
    • , Angela R Bradbury
    • , Judith S Brand
    • , Hiltrud Brauch
    • , Hermann Brenner
    • , Brigitte Bressac-de Paillerets
    • , Carole Brewer
    • , Louise Brinton
    • , Per Broberg
    • , Angela Brooks-Wilson
    • , Joan Brunet
    • , Thomas Brüning
    • , Barbara Burwinkel
    • , Saundra S Buys
    • , Jinyoung Byun
    • , Qiuyin Cai
    • , Trinidad Caldés
    • , Maria A Caligo
    • , Ian Campbell
    • , Federico Canzian
    • , Olivier Caron
    • , Angel Carracedo
    • , Brian D Carter
    • , J Esteban Castelao
    • , Laurent Castera
    • , Virginie Caux-Moncoutier
    • , Salina B Chan
    • , Jenny Chang-Claude
    • , Stephen J Chanock
    • , Xiaoqing Chen
    • , Ting-Yuan David Cheng
    • , Jocelyne Chiquette
    • , Hans Christiansen
    • , Kathleen B M Claes
    • , Christine L Clarke
    • , Thomas Conner
    • , Don M Conroy
    • , Jackie Cook
    • , Emilie Cordina-Duverger
    • , Sten Cornelissen
    • , Isabelle Coupier
    • , Angela Cox
    • , David G Cox
    • , Simon S Cross
    • , Katarina Cuk
    • , Julie M Cunningham
    • , Kamila Czene
    • , Mary B Daly
    • , Francesca Damiola
    • , Hatef Darabi
    • , Rosemarie Davidson
    • , Kim De Leeneer
    • , Peter Devilee
    • , Ed Dicks
    • , Orland Diez
    • , Yuan Chun Ding
    • , Nina Ditsch
    • , Kimberly F Doheny
    • , Susan M Domchek
    • , Cecilia M Dorfling
    • , Thilo Dörk
    • , Isabel dos-Santos-Silva
    • , Stéphane Dubois
    • , Pierre-Antoine Dugué
    • , Martine Dumont
    • , Alison M Dunning
    • , Lorraine Durcan
    • , Miriam Dwek
    • , Bernd Dworniczak
    • , Diana Eccles
    • , Ros Eeles
    • , Hans Ehrencrona
    • , Ursula Eilber
    • , Bent Ejlertsen
    • , Arif B Ekici
    • , A Heather Eliassen
    • , EMBRACE
    • , Christoph Engel
    • , Mikael Eriksson
    • , Laura Fachal
    • , Laurence Faivre
    • , Peter A Fasching
    • , Ulrike Faust
    • , Jonine Figueroa
    • , Dieter Flesch-Janys
    • , Olivia Fletcher
    • , Henrik Flyger
    • , William D Foulkes
    • , Eitan Friedman
    • , Lin Fritschi
    • , Debra Frost
    • , Marike Gabrielson
    • , Pragna Gaddam
    • , Marilie D Gammon
    • , Patricia A Ganz
    • , Susan M Gapstur
    • , Judy Garber
    • , Vanesa Garcia-Barberan
    • , José A García-Sáenz
    • , Mia M Gaudet
    • , Marion Gauthier-Villars
    • , Andrea Gehrig
    • , GEMO Study Collaborators
    • , Vassilios Georgoulias
    • , Anne-Marie Gerdes
    • , Graham G Giles
    • , Gord Glendon
    • , Andrew K Godwin
    • , Mark S Goldberg
    • , David E Goldgar
    • , Anna González-Neira
    • , Paul Goodfellow
    • , Mark H Greene
    • , Grethe I Grenaker Alnæs
    • , Mervi Grip
    • , Jacek Gronwald
    • , Anne Grundy
    • , Daphne Gschwantler-Kaulich
    • , Pascal Guénel
    • , Qi Guo
    • , Lothar Haeberle
    • , Eric Hahnen
    • , Christopher A Haiman
    • , Niclas Håkansson
    • , Emily Hallberg
    • , Ute Hamann
    • , Nathalie Hamel
    • , Susan Hankinson
    • , Thomas V O Hansen
    • , Patricia Harrington
    • , Steven N Hart
    • , Jaana M Hartikainen
    • , Catherine S Healey
    • , HEBON
    • , Alexander Hein
    • , Sonja Helbig
    • , Alex Henderson
    • , Jane Heyworth
    • , Belynda Hicks
    • , Peter Hillemanns
    • , Shirley Hodgson
    • , Frans B Hogervorst
    • , Antoinette Hollestelle
    • , Maartje J Hooning
    • , Bob Hoover
    • , John L Hopper
    • , Chunling Hu
    • , Guanmengqian Huang
    • , Peter J Hulick
    • , Keith Humphreys
    • , David J Hunter
    • , Evgeny N Imyanitov
    • , Claudine Isaacs
    • , Motoki Iwasaki
    • , Louise Izatt
    • , Anna Jakubowska
    • , Paul James
    • , Ramunas Janavicius
    • , Wolfgang Janni
    • , Uffe Birk Jensen
    • , Esther M John
    • , Nichola Johnson
    • , Kristine Jones
    • , Michael Jones
    • , Arja Jukkola-Vuorinen
    • , Rudolf Kaaks
    • , Maria Kabisch
    • , Katarzyna Kaczmarek
    • , Daehee Kang
    • , Karin Kast
    • , kConFab/AOCS Investigators
    • , Renske Keeman
    • , Michael J Kerin
    • , Carolien M Kets
    • , Machteld Keupers
    • , Sofia Khan
    • , Elza Khusnutdinova
    • , Johanna I Kiiski
    • , Sung-Won Kim
    • , Julia A Knight
    • , Irene Konstantopoulou
    • , Veli-Matti Kosma
    • , Vessela N Kristensen
    • , Torben A Kruse
    • , Ava Kwong
    • , Anne-Vibeke Lænkholm
    • , Yael Laitman
    • , Fiona Lalloo
    • , Diether Lambrechts
    • , Keren Landsman
    • , Christine Lasset
    • , Conxi Lazaro
    • , Loic Le Marchand
    • , Julie Lecarpentier
    • , Andrew Lee
    • , Eunjung Lee
    • , Jong Won Lee
    • , Min Hyuk Lee
    • , Flavio Lejbkowicz
    • , Fabienne Lesueur
    • , Jingmei Li
    • , Jenna Lilyquist
    • , Anne Lincoln
    • , Annika Lindblom
    • , Jolanta Lissowska
    • , Wing-Yee Lo
    • , Sibylle Loibl
    • , Jirong Long
    • , Jennifer T Loud
    • , Jan Lubinski
    • , Craig Luccarini
    • , Michael Lush
    • , Robert J MacInnis
    • , Tom Maishman
    • , Enes Makalic
    • , Ivana Maleva Kostovska
    • , Kathleen E Malone
    • , Siranoush Manoukian
    • , JoAnn E Manson
    • , Sara Margolin
    • , John W M Martens
    • , Maria Elena Martinez
    • , Keitaro Matsuo
    • , Dimitrios Mavroudis
    • , Sylvie Mazoyer
    • , Catriona McLean
    • , Hanne Meijers-Heijboer
    • , Primitiva Menéndez
    • , Jeffery Meyer
    • , Hui Miao
    • , Austin Miller
    • , Nicola Miller
    • , Gillian Mitchell
    • , Marco Montagna
    • , Kenneth Muir
    • , Anna Marie Mulligan
    • , Claire Mulot
    • , Sue Nadesan
    • , Katherine L Nathanson
    • , NBSC Collaborators
    • , Susan L Neuhausen
    • , Heli Nevanlinna
    • , Ines Nevelsteen
    • , Dieter Niederacher
    • , Sune F Nielsen
    • , Børge G Nordestgaard
    • , Aaron Norman
    • , Robert L Nussbaum
    • , Edith Olah
    • , Olufunmilayo I Olopade
    • , Janet E Olson
    • , Curtis Olswold
    • , Kai-ren Ong
    • , Jan C Oosterwijk
    • , Nick Orr
    • , Ana Osorio
    • , V Shane Pankratz
    • , Laura Papi
    • , Tjoung-Won Park-Simon
    • , Ylva Paulsson-Karlsson
    • , Rachel Lloyd
    • , Inge Søkilde Pedersen
    • , Bernard Peissel
    • , Ana Peixoto
    • , Jose I A Perez
    • , Paolo Peterlongo
    • , Julian Peto
    • , Georg Pfeiler
    • , Catherine M Phelan
    • , Mila Pinchev
    • , Dijana Plaseska-Karanfilska
    • , Bruce Poppe
    • , Mary E Porteous
    • , Ross Prentice
    • , Nadege Presneau
    • , Darya Prokofieva
    • , Elizabeth Pugh
    • , Miquel Angel Pujana
    • , Katri Pylkäs
    • , Brigitte Rack
    • , Paolo Radice
    • , Nazneen Rahman
    • , Johanna Rantala
    • , Christine Rappaport-Fuerhauser
    • , Gad Rennert
    • , Hedy S Rennert
    • , Valerie Rhenius
    • , Kerstin Rhiem
    • , Andrea Richardson
    • , Gustavo C Rodriguez
    • , Atocha Romero
    • , Jane Romm
    • , Matti A Rookus
    • , Anja Rudolph
    • , Thomas Ruediger
    • , Emmanouil Saloustros
    • , Joyce Sanders
    • , Dale P Sandler
    • , Suleeporn Sangrajrang
    • , Elinor J Sawyer
    • , Daniel F Schmidt
    • , Minouk J Schoemaker
    • , Fredrick Schumacher
    • , Peter Schürmann
    • , Lukas Schwentner
    • , Christopher Scott
    • , Rodney J Scott
    • , Sheila Seal
    • , Leigha Senter
    • , Caroline Seynaeve
    • , Mitul Shah
    • , Priyanka Sharma
    • , Chen-Yang Shen
    • , Xin Sheng
    • , Hermela Shimelis
    • , Martha J Shrubsole
    • , Xiao-Ou Shu
    • , Lucy E Side
    • , Christian F Singer
    • , Christof Sohn
    • , Melissa C Southey
    • , John J Spinelli
    • , Amanda B Spurdle
    • , Christa Stegmaier
    • , Dominique Stoppa-Lyonnet
    • , Grzegorz Sukiennicki
    • , Harald Surowy
    • , Christian Sutter
    • , Anthony Swerdlow
    • , Csilla I Szabo
    • , Rulla M Tamimi
    • , Yen Y Tan
    • , Jack A Taylor
    • , Maria-Isabel Tejada
    • , Maria Tengström
    • , Soo H Teo
    • , Mary B Terry
    • , Daniel C Tessier
    • , Alex Teulé
    • , Kathrin Thöne
    • , Darcy L Thull
    • , Maria Grazia Tibiletti
    • , Laima Tihomirova
    • , Marc Tischkowitz
    • , Amanda E Toland
    • , Rob A E M Tollenaar
    • , Ian Tomlinson
    • , Ling Tong
    • , Diana Torres
    • , Martine Tranchant
    • , Thérèse Truong
    • , Kathy Tucker
    • , Nadine Tung
    • , Jonathan Tyrer
    • , Hans-Ulrich Ulmer
    • , Celine Vachon
    • , Christi J van Asperen
    • , David Van Den Berg
    • , Ans M W van den Ouweland
    • , Elizabeth J van Rensburg
    • , Liliana Varesco
    • , Raymonda Varon-Mateeva
    • , Ana Vega
    • , Alessandra Viel
    • , Joseph Vijai
    • , Daniel Vincent
    • , Jason Vollenweider
    • , Lisa Walker
    • , Zhaoming Wang
    • , Shan Wang-Gohrke
    • , Barbara Wappenschmidt
    • , Clarice R Weinberg
    • , Jeffrey N Weitzel
    • , Camilla Wendt
    • , Jelle Wesseling
    • , Alice S Whittemore
    • , Juul T Wijnen
    • , Walter Willett
    • , Robert Winqvist
    • , Alicja Wolk
    • , Anna H Wu
    • , Lucy Xia
    • , Xiaohong R Yang
    • , Drakoulis Yannoukakos
    • , Daniela Zaffaroni
    • , Wei Zheng
    • , Bin Zhu
    • , Argyrios Ziogas
    • , Elad Ziv
    • , Kristin K Zorn
    • , Manuela Gago-Dominguez
    • , Arto Mannermaa
    • , Håkan Olsson
    • , Manuel R Teixeira
    • , Jennifer Stone
    • , Kenneth Offit
    • , Laura Ottini
    • , Sue K Park
    • , Mads Thomassen
    • , Per Hall
    • , Alfons Meindl
    • , Rita K Schmutzler
    • , Arnaud Droit
    • , Gary D Bader
    • , Paul D P Pharoah
    • , Fergus J Couch
    • , Douglas F Easton
    • , Peter Kraft
    • , Georgia Chenevix-Trench
    • , Montserrat García-Closas
    • , Marjanka K Schmidt
    • , Antonis C Antoniou
    •  & Jacques Simard
  • Analysis |

    This study presents a new approach to estimate the tissues contributing to the genetic causality for complex traits and diseases. The method assesses tissue sharing of eQTLs among 44 tissues and then uses these tissue-sharing estimates to infer the tissues where trait-associated variants likely exert their function.

    • Halit Ongen
    • , Andrew A Brown
    • , Olivier Delaneau
    • , Nikolaos I Panousis
    • , Alexandra C Nica
    • , GTEx Consortium
    •  & Emmanouil T Dermitzakis
  • Letter |

    CaVEMaN is a new method that uses whole-genome sequencing and RNA-sequencing data to implicate likely causal variants affecting gene expression. The set of high-confidence causal variants found in multiple tissues is enriched for variants associated with complex traits.

    • Andrew Anand Brown
    • , Ana Viñuela
    • , Olivier Delaneau
    • , Tim D Spector
    • , Kerrin S Small
    •  & Emmanouil T Dermitzakis
  • Article |

    Analysis of a large bread-wheat genomic data set through a quantitative genetic framework designed to study the genetic basis of heterosis shows that hybrids outperform midparents in grain yield by 10%. Genome-wide prediction and association mapping indicate that epistasis plays a significant role in heterosis of grain yield in wheat.

    • Yong Jiang
    • , Renate H Schmidt
    • , Yusheng Zhao
    •  & Jochen C Reif
  • Technical Report |

    Covariates for multiphenotype studies (CMS), a new approach for testing for associations from large-scale datasets, leverages genetic and environmental factors shared between correlated variables measured on the same samples. Applying CMS to real and simulated data demonstrates a large increase in power equivalent to that gained by doubling the sample size.

    • Hugues Aschard
    • , Vincent Guillemot
    • , Bjarni Vilhjalmsson
    • , Chirag J Patel
    • , David Skurnik
    • , Chun J Ye
    • , Brian Wolpin
    • , Peter Kraft
    •  & Noah Zaitlen
  • Article |

    A genome-wide association analysis using data from Chinese individuals combined with a transethnic meta-analysis of Psychiatry Genomics Consortium data identifies 30 new loci for schizophrenia. These analyses improve the fine-mapping of susceptibility loci and implicate multiple pathways in schizophrenia biology.

    • Zhiqiang Li
    • , Jianhua Chen
    • , Hao Yu
    • , Lin He
    • , Yifeng Xu
    • , Dai Zhang
    • , Qizhong Yi
    • , Changgui Li
    • , Xingwang Li
    • , Jiawei Shen
    • , Zhijian Song
    • , Weidong Ji
    • , Meng Wang
    • , Juan Zhou
    • , Boyu Chen
    • , Yahui Liu
    • , Jiqiang Wang
    • , Peng Wang
    • , Ping Yang
    • , Qingzhong Wang
    • , Guoyin Feng
    • , Benxiu Liu
    • , Wensheng Sun
    • , Baojie Li
    • , Guang He
    • , Weidong Li
    • , Chunling Wan
    • , Qi Xu
    • , Wenjin Li
    • , Zujia Wen
    • , Ke Liu
    • , Fang Huang
    • , Jue Ji
    • , Stephan Ripke
    • , Weihua Yue
    • , Patrick F Sullivan
    • , Michael C O'Donovan
    •  & Yongyong Shi
  • Article |

    Exome sequencing of 2,871 probands with congenital heart disease (CHD) provides new insights into the genetic architecture of these disorders. The results implicate new genes in CHD pathogenesis and highlight striking overlap between genes with damaging de novo mutations in individuals with CHD and autism.

    • Sheng Chih Jin
    • , Jason Homsy
    • , Samir Zaidi
    • , Qiongshi Lu
    • , Sarah Morton
    • , Steven R DePalma
    • , Xue Zeng
    • , Hongjian Qi
    • , Weni Chang
    • , Michael C Sierant
    • , Wei-Chien Hung
    • , Shozeb Haider
    • , Junhui Zhang
    • , James Knight
    • , Robert D Bjornson
    • , Christopher Castaldi
    • , Irina R Tikhonoa
    • , Kaya Bilguvar
    • , Shrikant M Mane
    • , Stephan J Sanders
    • , Seema Mital
    • , Mark W Russell
    • , J William Gaynor
    • , John Deanfield
    • , Alessandro Giardini
    • , George A Porter Jr
    • , Deepak Srivastava
    • , Cecelia W Lo
    • , Yufeng Shen
    • , W Scott Watkins
    • , Mark Yandell
    • , H Joseph Yost
    • , Martin Tristani-Firouzi
    • , Jane W Newburger
    • , Amy E Roberts
    • , Richard Kim
    • , Hongyu Zhao
    • , Jonathan R Kaltman
    • , Elizabeth Goldmuntz
    • , Wendy K Chung
    • , Jonathan G Seidman
    • , Bruce D Gelb
    • , Christine E Seidman
    • , Richard P Lifton
    •  & Martina Brueckner
  • Article | | open

    The assembly of the durian genome provides insights into the unique flavor profile of this tropical fruit. Transcriptome and metabolome analyses show that methionine γ-lyase is upregulated and that volatile sulfur compounds are produced during ripening.

    • Bin Tean Teh
    • , Kevin Lim
    • , Chern Han Yong
    • , Cedric Chuan Young Ng
    • , Sushma Ramesh Rao
    • , Vikneswari Rajasegaran
    • , Weng Khong Lim
    • , Choon Kiat Ong
    • , Ki Chan
    • , Vincent Kin Yuen Cheng
    • , Poh Sheng Soh
    • , Sanjay Swarup
    • , Steven G Rozen
    • , Niranjan Nagarajan
    •  & Patrick Tan
  • Analysis |

    This large-scale analysis of copy number alterations (CNAs) in patient-derived xenografts (PDXs) across 24 cancer types shows that new CNAs accumulate quickly and that the specific CNAs acquired during passaging differ from those acquired during tumor evolution in patients, suggesting that PDX tumors are under distinct selection pressures from tumors in human hosts.

    • Uri Ben-David
    • , Gavin Ha
    • , Yuen-Yi Tseng
    • , Noah F Greenwald
    • , Coyin Oh
    • , Juliann Shih
    • , James M McFarland
    • , Bang Wong
    • , Jesse S Boehm
    • , Rameen Beroukhim
    •  & Todd R Golub
  • Letter |

    Ali Shilatifard and colleagues generate Drosophila lines expressing catalytically deficient Trr, which normally deposits H3K4me1 at enhancers. Trr mutants undergo normal development and show minimal changes in gene expression.

    • Ryan Rickels
    • , Hans-Martin Herz
    • , Christie C Sze
    • , Kaixiang Cao
    • , Marc A Morgan
    • , Clayton K Collings
    • , Maria Gause
    • , Yoh-hei Takahashi
    • , Lu Wang
    • , Emily J Rendleman
    • , Stacy A Marshall
    • , Annika Krueger
    • , Elizabeth T Bartom
    • , Andrea Piunti
    • , Edwin R Smith
    • , Nebiyu A Abshiru
    • , Neil L Kelleher
    • , Dale Dorsett
    •  & Ali Shilatifard
  • Corrigendum |

    • Helen R Warren
    • , Evangelos Evangelou
    • , Claudia P Cabrera
    • , He Gao
    • , Meixia Ren
    • , Borbala Mifsud
    • , Ioanna Ntalla
    • , Praveen Surendran
    • , Chunyu Liu
    • , James P Cook
    • , Aldi T Kraja
    • , Fotios Drenos
    • , Marie Loh
    • , Niek Verweij
    • , Jonathan Marten
    • , Ibrahim Karaman
    • , Marcelo P Segura Lepe
    • , Paul F O'Reilly
    • , Joanne Knight
    • , Harold Snieder
    • , Norihiro Kato
    • , Jiang He
    • , E Shyong Tai
    • , M Abdullah Said
    • , David Porteous
    • , Maris Alver
    • , Neil Poulter
    • , Martin Farrall
    • , Ron T Gansevoort
    • , Sandosh Padmanabhan
    • , Reedik Mägi
    • , Alice Stanton
    • , John Connell
    • , Stephan J L Bakker
    • , Andres Metspalu
    • , Denis C Shields
    • , Simon Thom
    • , Morris Brown
    • , Peter Sever
    • , Tõnu Esko
    • , Caroline Hayward
    • , Pim van der Harst
    • , Danish Saleheen
    • , Rajiv Chowdhury
    • , John C Chambers
    • , Daniel I Chasman
    • , Aravinda Chakravarti
    • , Christopher Newton-Cheh
    • , Cecilia M Lindgren
    • , Daniel Levy
    • , Jaspal S Kooner
    • , Bernard Keavney
    • , Maciej Tomaszewski
    • , Nilesh J Samani
    • , Joanna M M Howson
    • , Martin D Tobin
    • , Patricia B Munroe
    • , Georg B Ehret
    • , Louise V Wain
    • , The International Consortium of Blood Pressure (ICBP) 1000G Analyses, The CHD Exome+ Consortium, The ExomeBP Consortium, The T2D-GENES Consortium, The GoT2DGenes Consortium, The Cohorts for Heart and Ageing Research in Genome Epidemiology (CHARGE) BP Exome Consortium, The International Genomics of Blood Pressure (iGEN-BP) Consortium
    • , Michael R Barnes
    • , Ioanna Tzoulaki
    • , Mark J Caulfield
    • , Paul Elliott
    •  & for The UK Biobank CardioMetabolic Consortium BP working group
  • Erratum |

    • Suzanne Sniekers
    • , Sven Stringer
    • , Kyoko Watanabe
    • , Philip R Jansen
    • , Jonathan R I Coleman
    • , Eva Krapohl
    • , Erdogan Taskesen
    • , Anke R Hammerschlag
    • , Aysu Okbay
    • , Delilah Zabaneh
    • , Najaf Amin
    • , Gerome Breen
    • , David Cesarini
    • , Christopher F Chabris
    • , William G Iacono
    • , M Arfan Ikram
    • , Magnus Johannesson
    • , Philipp Koellinger
    • , James J Lee
    • , Patrik K E Magnusson
    • , Matt McGue
    • , Mike B Miller
    • , William E R Ollier
    • , Antony Payton
    • , Neil Pendleton
    • , Robert Plomin
    • , Cornelius A Rietveld
    • , Henning Tiemeier
    • , Cornelia M van Duijn
    •  & Danielle Posthuma