Volume 51 Issue 2, February 2019

Volume 51 Issue 2

Fields of gold

Analysis of genomic data for the entire barley collection of the German Federal ex situ Genebank provides insights into the population structure of domesticated barley and helps link natural variation to human selection during crop evolution.

See Milner et al.

Image: Photograph by Nils Stein. Cover Design: Erin Dewalt.

Editorial

  • Editorial |

    Ensuring that agricultural production meets the goal of feeding a world experiencing continued human population growth and increasingly severe effects from climate change is an urgent challenge. Genomics has a role to play in maximizing the utility, diversity and yield of resources, as well as in contributing to sustained food security in the future.

Correspondence

News & Views

  • News & Views |

    Contemporary genomics and informatics technologies were used to provide a meaningful and insightful overview of more than 20,000 wild and domesticated barley genotypes from one of the largest crop germplasm collections. The data provide a framework for the rational exploitation of genetic resources in crop improvement, which will be central to addressing global food security.

    • Peter Langridge
    •  & Robbie Waugh

Letters

  • Letter |

    Analysis of advanced cancer patients treated with immune-checkpoint inhibitors shows that tumor mutational burden, as assessed by targeted next-generation sequencing, predicts survival after immunotherapy across multiple cancer types.

    • Robert M. Samstein
    • , Chung-Han Lee
    • , Alexander N. Shoushtari
    • , Matthew D. Hellmann
    • , Ronglai Shen
    • , Yelena Y. Janjigian
    • , David A. Barron
    • , Ahmet Zehir
    • , Emmet J. Jordan
    • , Antonio Omuro
    • , Thomas J. Kaley
    • , Sviatoslav M. Kendall
    • , Robert J. Motzer
    • , A. Ari Hakimi
    • , Martin H. Voss
    • , Paul Russo
    • , Jonathan Rosenberg
    • , Gopa Iyer
    • , Bernard H. Bochner
    • , Dean F. Bajorin
    • , Hikmat A. Al-Ahmadie
    • , Jamie E. Chaft
    • , Charles M. Rudin
    • , Gregory J. Riely
    • , Shrujal Baxi
    • , Alan L. Ho
    • , Richard J. Wong
    • , David G. Pfister
    • , Jedd D. Wolchok
    • , Christopher A. Barker
    • , Philip H. Gutin
    • , Cameron W. Brennan
    • , Viviane Tabar
    • , Ingo K. Mellinghoff
    • , Lisa M. DeAngelis
    • , Charlotte E. Ariyan
    • , Nancy Lee
    • , William D. Tap
    • , Mrinal M. Gounder
    • , Sandra P. D’Angelo
    • , Leonard Saltz
    • , Zsofia K. Stadler
    • , Howard I. Scher
    • , Jose Baselga
    • , Pedram Razavi
    • , Christopher A. Klebanoff
    • , Rona Yaeger
    • , Neil H. Segal
    • , Geoffrey Y. Ku
    • , Ronald P. DeMatteo
    • , Marc Ladanyi
    • , Naiyer A. Rizvi
    • , Michael F. Berger
    • , Nadeem Riaz
    • , David B. Solit
    • , Timothy A. Chan
    •  & Luc G. T. Morris
  • Letter |

    Activating HER2 mutations are shown to confer resistance to ER-directed therapies in patients with ER+ metastatic breast cancer. Drug resistance caused by HER2 mutations was overcome by combining ER-directed therapy with a HER2 kinase inhibitor.

    • Utthara Nayar
    • , Ofir Cohen
    • , Christian Kapstad
    • , Michael S. Cuoco
    • , Adrienne G. Waks
    • , Seth A. Wander
    • , Corrie Painter
    • , Samuel Freeman
    • , Nicole S. Persky
    • , Lori Marini
    • , Karla Helvie
    • , Nelly Oliver
    • , Orit Rozenblatt-Rosen
    • , Cynthia X. Ma
    • , Aviv Regev
    • , Eric P. Winer
    • , Nancy U. Lin
    •  & Nikhil Wagle
  • Letter |

    GADD45A directly binds to R-loops and mediates local DNA demethylation by recruiting TET1. lncRNA-mediated formation of R-loops at the promoter of the tumor suppressor TCF21 triggers GADD45A binding, demethylation and expression.

    • Khelifa Arab
    • , Emil Karaulanov
    • , Michael Musheev
    • , Philipp Trnka
    • , Andrea Schäfer
    • , Ingrid Grummt
    •  & Christof Niehrs
  • Letter | | open

    The improved genome assemblies of allotetraploid cotton species Gossypium hirsutum and Gossypium barbadense provide insights into cotton evolution and inform the construction of introgression lines used to identify loci associated with fiber quality.

    • Maojun Wang
    • , Lili Tu
    • , Daojun Yuan
    • , De Zhu
    • , Chao Shen
    • , Jianying Li
    • , Fuyan Liu
    • , Liuling Pei
    • , Pengcheng Wang
    • , Guannan Zhao
    • , Zhengxiu Ye
    • , Hui Huang
    • , Feilin Yan
    • , Yizan Ma
    • , Lin Zhang
    • , Min Liu
    • , Jiaqi You
    • , Yicheng Yang
    • , Zhenping Liu
    • , Fan Huang
    • , Baoqi Li
    • , Ping Qiu
    • , Qinghua Zhang
    • , Longfu Zhu
    • , Shuangxia Jin
    • , Xiyan Yang
    • , Ling Min
    • , Guoliang Li
    • , Ling-Ling Chen
    • , Hongkun Zheng
    • , Keith Lindsey
    • , Zhongxu Lin
    • , Joshua A. Udall
    •  & Xianlong Zhang
  • Letter |

    Genome-wide meta-analysis of UK Biobank and arcOGEN (77,052 cases and 378,169 controls) identifies 52 new osteoarthritis risk loci. Integrated eQTL colocalization, fine-mapping, and rare-disease data identify putative effector genes for osteoarthritis.

    • Ioanna Tachmazidou
    • , Konstantinos Hatzikotoulas
    • , Lorraine Southam
    • , Jorge Esparza-Gordillo
    • , Valeriia Haberland
    • , Jie Zheng
    • , Toby Johnson
    • , Mine Koprulu
    • , Eleni Zengini
    • , Julia Steinberg
    • , Jeremy M. Wilkinson
    • , Sahir Bhatnagar
    • , Joshua D. Hoffman
    • , Natalie Buchan
    • , Dániel Süveges
    • , Laura Yerges-Armstrong
    • , George Davey Smith
    • , Tom R. Gaunt
    • , Robert A. Scott
    • , Linda C. McCarthy
    •  & Eleftheria Zeggini
  • Letter |

    Association studies of up to 1.2 million individuals identify 566 genetic variants in 406 loci associated with tobacco use and addiction (initiation, cessation, and heaviness) as well as alcohol use, with 150 loci showing pleiotropic association.

    • Mengzhen Liu
    • , Yu Jiang
    • , Robbee Wedow
    • , Yue Li
    • , David M. Brazel
    • , Fang Chen
    • , Gargi Datta
    • , Jose Davila-Velderrain
    • , Daniel McGuire
    • , Chao Tian
    • , Xiaowei Zhan
    • , Michelle Agee
    • , Babak Alipanahi
    • , Adam Auton
    • , Robert K. Bell
    • , Katarzyna Bryc
    • , Sarah L. Elson
    • , Pierre Fontanillas
    • , Nicholas A. Furlotte
    • , David A. Hinds
    • , Bethann S. Hromatka
    • , Karen E. Huber
    • , Aaron Kleinman
    • , Nadia K. Litterman
    • , Matthew H. McIntyre
    • , Joanna L. Mountain
    • , Carrie A. M. Northover
    • , J. Fah Sathirapongsasuti
    • , Olga V. Sazonova
    • , Janie F. Shelton
    • , Suyash Shringarpure
    • , Chao Tian
    • , Joyce Y. Tung
    • , Vladimir Vacic
    • , Catherine H. Wilson
    • , Steven J. Pitts
    • , Amy Mitchell
    • , Anne Heidi Skogholt
    • , Bendik S. Winsvold
    • , Børge Sivertsen
    • , Eystein Stordal
    • , Gunnar Morken
    • , Håvard Kallestad
    • , Ingrid Heuch
    • , John-Anker Zwart
    • , Katrine Kveli Fjukstad
    • , Linda M. Pedersen
    • , Maiken Elvestad Gabrielsen
    • , Marianne Bakke Johnsen
    • , Marit Skrove
    • , Marit Sæbø Indredavik
    • , Ole Kristian Drange
    • , Ottar Bjerkeset
    • , Sigrid Børte
    • , Synne Øien Stensland
    • , Hélène Choquet
    • , Anna R. Docherty
    • , Jessica D. Faul
    • , Johanna R. Foerster
    • , Lars G. Fritsche
    • , Maiken Elvestad Gabrielsen
    • , Scott D. Gordon
    • , Jeffrey Haessler
    • , Jouke-Jan Hottenga
    • , Hongyan Huang
    • , Seon-Kyeong Jang
    • , Philip R. Jansen
    • , Yueh Ling
    • , Reedik Mägi
    • , Nana Matoba
    • , George McMahon
    • , Antonella Mulas
    • , Valeria Orrù
    • , Teemu Palviainen
    • , Anita Pandit
    • , Gunnar W. Reginsson
    • , Anne Heidi Skogholt
    • , Jennifer A. Smith
    • , Amy E. Taylor
    • , Constance Turman
    • , Gonneke Willemsen
    • , Hannah Young
    • , Kendra A. Young
    • , Gregory J. M. Zajac
    • , Wei Zhao
    • , Wei Zhou
    • , Gyda Bjornsdottir
    • , Jason D. Boardman
    • , Michael Boehnke
    • , Dorret I. Boomsma
    • , Chu Chen
    • , Francesco Cucca
    • , Gareth E. Davies
    • , Charles B. Eaton
    • , Marissa A. Ehringer
    • , Tõnu Esko
    • , Edoardo Fiorillo
    • , Nathan A. Gillespie
    • , Daniel F. Gudbjartsson
    • , Toomas Haller
    • , Kathleen Mullan Harris
    • , Andrew C. Heath
    • , John K. Hewitt
    • , Ian B. Hickie
    • , John E. Hokanson
    • , Christian J. Hopfer
    • , David J. Hunter
    • , William G. Iacono
    • , Eric O. Johnson
    • , Yoichiro Kamatani
    • , Sharon L. R. Kardia
    • , Matthew C. Keller
    • , Manolis Kellis
    • , Charles Kooperberg
    • , Peter Kraft
    • , Kenneth S. Krauter
    • , Markku Laakso
    • , Penelope A. Lind
    • , Anu Loukola
    • , Sharon M. Lutz
    • , Pamela A. F. Madden
    • , Nicholas G. Martin
    • , Matt McGue
    • , Matthew B. McQueen
    • , Sarah E. Medland
    • , Andres Metspalu
    • , Karen L. Mohlke
    • , Jonas B. Nielsen
    • , Yukinori Okada
    • , Ulrike Peters
    • , Tinca J. C. Polderman
    • , Danielle Posthuma
    • , Alexander P. Reiner
    • , John P. Rice
    • , Eric Rimm
    • , Richard J. Rose
    • , Valgerdur Runarsdottir
    • , Michael C. Stallings
    • , Alena Stančáková
    • , Hreinn Stefansson
    • , Khanh K. Thai
    • , Hilary A. Tindle
    • , Thorarinn Tyrfingsson
    • , Tamara L. Wall
    • , David R. Weir
    • , Constance Weisner
    • , John B. Whitfield
    • , Bendik Slagsvold Winsvold
    • , Jie Yin
    • , Luisa Zuccolo
    • , Laura J. Bierut
    • , Kristian Hveem
    • , James J. Lee
    • , Marcus R. Munafò
    • , Nancy L. Saccone
    • , Cristen J. Willer
    • , Marilyn C. Cornelis
    • , Sean P. David
    • , David A. Hinds
    • , Eric Jorgenson
    • , Jaakko Kaprio
    • , Jerry A. Stitzel
    • , Kari Stefansson
    • , Thorgeir E. Thorgeirsson
    • , Gonçalo Abecasis
    • , Dajiang J. Liu
    •  & Scott Vrieze

Articles

  • Article |

    A genetic study identifies hundreds of loci associated with risk tolerance and risky behaviors, finds evidence of substantial shared genetic influences across these phenotypes, and implicates genes involved in neurotransmission.

    • Richard Karlsson Linnér
    • , Pietro Biroli
    • , Edward Kong
    • , S. Fleur W. Meddens
    • , Robbee Wedow
    • , Mark Alan Fontana
    • , Maël Lebreton
    • , Stephen P. Tino
    • , Abdel Abdellaoui
    • , Anke R. Hammerschlag
    • , Michel G. Nivard
    • , Aysu Okbay
    • , Cornelius A. Rietveld
    • , Pascal N. Timshel
    • , Maciej Trzaskowski
    • , Ronald de Vlaming
    • , Christian L. Zünd
    • , Yanchun Bao
    • , Laura Buzdugan
    • , Ann H. Caplin
    • , Chia-Yen Chen
    • , Peter Eibich
    • , Pierre Fontanillas
    • , Juan R. Gonzalez
    • , Peter K. Joshi
    • , Ville Karhunen
    • , Aaron Kleinman
    • , Remy Z. Levin
    • , Christina M. Lill
    • , Gerardus A. Meddens
    • , Gerard Muntané
    • , Sandra Sanchez-Roige
    • , Frank J. van Rooij
    • , Erdogan Taskesen
    • , Yang Wu
    • , Futao Zhang
    • , Michelle Agee
    • , Babak Alipanahi
    • , Robert K. Bell
    • , Katarzyna Bryc
    • , Sarah L. Elson
    • , Nicholas A. Furlotte
    • , Karen E. Huber
    • , Nadia K. Litterman
    • , Jennifer C. McCreight
    • , Matthew H. McIntyre
    • , Joanna L. Mountain
    • , Carrie A. M. Northover
    • , Steven J. Pitts
    • , J. Fah Sathirapongsasuti
    • , Olga V. Sazonova
    • , Janie F. Shelton
    • , Suyash Shringarpure
    • , Chao Tian
    • , Joyce Y. Tung
    • , Vladimir Vacic
    • , Catherine H. Wilson
    • , Mawussé Agbessi
    • , Habibul Ahsan
    • , Isabel Alves
    • , Anand Andiappan
    • , Philip Awadalla
    • , Alexis Battle
    • , Frank Beutner
    • , Marc Jan Bonder
    • , Dorret I. Boomsma
    • , Mark Christiansen
    • , Annique Claringbould
    • , Patrick Deelen
    • , Tõnu Esko
    • , Marie-Julie Favé
    • , Lude Franke
    • , Timothy Frayling
    • , Sina A. Gharib
    • , Gregory Gibson
    • , Bastiaan Heijmans
    • , Gibran Hemani
    • , Rick Jansen
    • , Mika Kähönen
    • , Anette Kalnapenkis
    • , Silva Kasela
    • , Johannes Kettunen
    • , Yungil Kim
    • , Holger Kirsten
    • , Peter Kovacs
    • , Knut Krohn
    • , Jaanika Kronberg-Guzman
    • , Viktorija Kukushkina
    • , Zoltan Kutalik
    • , Bernett Lee
    • , Terho Lehtimäki
    • , Markus Loeffler
    • , Urko M. Marigorta
    • , Andres Metspalu
    • , Lili Milani
    • , Grant W. Montgomery
    • , Martina Müller-Nurasyid
    • , Matthias Nauck
    • , Michel G. Nivard
    • , Brenda Penninx
    • , Markus Perola
    • , Natalia Pervjakova
    • , Brandon Pierce
    • , Joseph Powell
    • , Holger Prokisch
    • , Bruce M. Psaty
    • , Olli Raitakari
    • , Susan Ring
    • , Samuli Ripatti
    • , Olaf Rotzchke
    • , Sina Rüeger
    • , Ashis Saha
    • , Markus Scholz
    • , Katharina Schramm
    • , Ilkka Seppälä
    • , Michael Stumvoll
    • , Patrick Sullivan
    • , Peter-Bram t Hoen
    • , Alexander Teumer
    • , Joachim Thiery
    • , Lin Tong
    • , Anke Tönjes
    • , Jenny van Dongen
    • , Joyce van Meurs
    • , Joost Verlouw
    • , Peter M. Visscher
    • , Uwe Völker
    • , Urmo Võsa
    • , Harm-Jan Westra
    • , Hanieh Yaghootkar
    • , Jian Yang
    • , Biao Zeng
    • , Futao Zhang
    • , Aysu Okbay
    • , Jonathan P. Beauchamp
    • , Mark Alan Fontana
    • , James J. Lee
    • , Tune H. Pers
    • , Cornelius A. Rietveld
    • , Patrick Turley
    • , Guo-Bo Chen
    • , Valur Emilsson
    • , S. Fleur W. Meddens
    • , Sven Oskarsson
    • , Joseph K. Pickrell
    • , Kevin Thom
    • , Pascal Timshel
    • , Ronald de Vlaming
    • , Abdel Abdellaoui
    • , Tarunveer S. Ahluwalia
    • , Jonas Bacelis
    • , Clemens Baumbach
    • , Gyda Bjornsdottir
    • , Johannes H. Brandsma
    • , Maria Pina Concas
    • , Jaime Derringer
    • , Nicholas A. Furlotte
    • , Tessel E. Galesloot
    • , Giorgia Girotto
    • , Richa Gupta
    • , Leanne M. Hall
    • , Sarah E. Harris
    • , Edith Hofer
    • , Momoko Horikoshi
    • , Jennifer E. Huffman
    • , Kadri Kaasik
    • , Ioanna P. Kalafati
    • , Robert Karlsson
    • , Augustine Kong
    • , Jari Lahti
    • , Sven J. van der Lee
    • , Christiaan de Leeuw
    • , Penelope A. Lind
    • , Karl-Oskar Lindgren
    • , Tian Liu
    • , Massimo Mangino
    • , Jonathan Marten
    • , Evelin Mihailov
    • , Michael B. Miller
    • , Peter J. van der Most
    • , Christopher Oldmeadow
    • , Antony Payton
    • , Natalia Pervjakova
    • , Wouter J. Peyrot
    • , Yong Qian
    • , Olli Raitakari
    • , Rico Rueedi
    • , Erika Salvi
    • , Börge Schmidt
    • , Katharina E. Schraut
    • , Jianxin Shi
    • , Albert V. Smith
    • , Raymond A. Poot
    • , Beate St Pourcain
    • , Alexander Teumer
    • , Gudmar Thorleifsson
    • , Niek Verweij
    • , Dragana Vuckovic
    • , Juergen Wellmann
    • , Harm-Jan Westra
    • , Jingyun Yang
    • , Wei Zhao
    • , Zhihong Zhu
    • , Behrooz Z. Alizadeh
    • , Najaf Amin
    • , Andrew Bakshi
    • , Sebastian E. Baumeister
    • , Ginevra Biino
    • , Klaus Bønnelykke
    • , Patricia A. Boyle
    • , Harry Campbell
    • , Francesco P. Cappuccio
    • , Gail Davies
    • , Jan-Emmanuel De Neve
    • , Panos Deloukas
    • , Ilja Demuth
    • , Jun Ding
    • , Peter Eibich
    • , Lewin Eisele
    • , Niina Eklund
    • , David M. Evans
    • , Jessica D. Faul
    • , Mary F. Feitosa
    • , Andreas J. Forstner
    • , Ilaria Gandin
    • , Bjarni Gunnarsson
    • , Bjarni V. Halldórsson
    • , Tamara B. Harris
    • , Andrew C. Heath
    • , Lynne J. Hocking
    • , Elizabeth G. Holliday
    • , Georg Homuth
    • , Michael A. Horan
    • , Jouke-Jan Hottenga
    • , Philip L. de Jager
    • , Peter K. Joshi
    • , Astanand Jugessur
    • , Marika A. Kaakinen
    • , Mika Kähönen
    • , Stavroula Kanoni
    • , Liisa Keltigangas-Järvinen
    • , Lambertus A. L. M. Kiemeney
    • , Ivana Kolcic
    • , Seppo Koskinen
    • , Aldi T. Kraja
    • , Martin Kroh
    • , Zoltan Kutalik
    • , Antti Latvala
    • , Lenore J. Launer
    • , Maël P. Lebreton
    • , Douglas F. Levinson
    • , Paul Lichtenstein
    • , Peter Lichtner
    • , David C. M. Liewald
    • , Anu Loukola
    • , Pamela A. Madden
    • , Reedik Mägi
    • , Tomi Mäki-Opas
    • , Riccardo E. Marioni
    • , Pedro Marques-Vidal
    • , Gerardus A. Meddens
    • , George McMahon
    • , Christa Meisinger
    • , Thomas Meitinger
    • , Yusplitri Milaneschi
    • , Lili Milani
    • , Grant W. Montgomery
    • , Ronny Myhre
    • , Christopher P. Nelson
    • , Dale R. Nyholt
    • , William E. R. Ollier
    • , Aarno Palotie
    • , Lavinia Paternoster
    • , Nancy L. Pedersen
    • , Katja E. Petrovic
    • , David J. Porteous
    • , Katri Räikkönen
    • , Susan M. Ring
    • , Antonietta Robino
    • , Olga Rostapshova
    • , Igor Rudan
    • , Aldo Rustichini
    • , Veikko Salomaa
    • , Alan R. Sanders
    • , Antti-Pekka Sarin
    • , Helena Schmidt
    • , Rodney J. Scott
    • , Blair H. Smith
    • , Jennifer A. Smith
    • , Jan A. Staessen
    • , Elisabeth Steinhagen-Thiessen
    • , Konstantin Strauch
    • , Antonio Terracciano
    • , Martin D. Tobin
    • , Sheila Ulivi
    • , Simona Vaccargiu
    • , Lydia Quaye
    • , Frank J. van Rooij
    • , Cristina Venturini
    • , Anna A. E. Vinkhuyzen
    • , Uwe Völker
    • , Henry Völzke
    • , Judith M. Vonk
    • , Diego Vozzi
    • , Johannes Waage
    • , Erin B. Ware
    • , Gonneke Willemsen
    • , John R. Attia
    • , David A. Bennett
    • , Klaus Berger
    • , Lars Bertram
    • , Hans Bisgaard
    • , Dorret I. Boomsma
    • , Ingrid B Borecki
    • , Ute Bültmann
    • , Christopher F. Chabris
    • , Francesco Cucca
    • , Daniele Cusi
    • , Ian J. Deary
    • , George V. Dedoussis
    • , Cornelia M. van Duijn
    • , Johan G. Eriksson
    • , Barbara Franke
    • , Lude Franke
    • , Paolo Gasparini
    • , Pablo V. Gejman
    • , Christian Gieger
    • , Hans-Jörgen Grabe
    • , Jacob Gratten
    • , Patrick J. F. Groenen
    • , Vilmundur Gudnason
    • , Pim van der Harst
    • , Caroline Hayward
    • , David A. Hinds
    • , Wolfgang Hoffmann
    • , Elina Hyppönen
    • , William G. Iacono
    • , Bo Jacobsson
    • , Marjo-Riitta Järvelin
    • , Karl-Heinz Jöckel
    • , Jaakko Kaprio
    • , Sharon L. R. Kardia
    • , Terho Lehtimäki
    • , Steven F. Lehrer
    • , Patrik K. E. Magnusson
    • , Nicholas G. Martin
    • , Matt McGue
    • , Andres Metspalu
    • , Neil Pendleton
    • , Brenda Penninx
    • , Markus Perola
    • , Nicola Pirastu
    • , Mario Pirastu
    • , Ozren Polasek
    • , Danielle Posthuma
    • , Christine Power
    • , Michael A. Province
    • , Nilesh J. Samani
    • , David Schlessinger
    • , Reinhold Schmidt
    • , Thorkild I. A. Sørensen
    • , Tim D. Spector
    • , Kari Stefansson
    • , Unnur Thorsteinsdottir
    • , A. Roy Thurik
    • , Nicholas J. Timpson
    • , Henning Tiemeier
    • , Joyce Y. Tung
    • , André G. Uitterlinden
    • , Veronique Vitart
    • , Peter Vollenweider
    • , David R. Weir
    • , James F. Wilson
    • , Alan F. Wright
    • , Dalton C. Conley
    • , Robert F. Krueger
    • , George Davey Smith
    • , Albert Hofman
    • , David I. Laibson
    • , Sarah E. Medland
    • , Michelle N. Meyer
    • , Jian Yang
    • , Magnus Johannesson
    • , Peter M. Visscher
    • , Tõnu Esko
    • , Philipp D. Koellinger
    • , David Cesarini
    • , Daniel J. Benjamin
    • , Adam Auton
    • , Jason D. Boardman
    • , David W. Clark
    • , Andrew Conlin
    • , Conor C. Dolan
    • , Urs Fischbacher
    • , Patrick J. F. Groenen
    • , Kathleen Mullan Harris
    • , Gregor Hasler
    • , Albert Hofman
    • , Mohammad A. Ikram
    • , Sonia Jain
    • , Robert Karlsson
    • , Ronald C. Kessler
    • , Maarten Kooyman
    • , James MacKillop
    • , Minna Männikkö
    • , Carlos Morcillo-Suarez
    • , Matthew B. McQueen
    • , Klaus M. Schmidt
    • , Melissa C. Smart
    • , Matthias Sutter
    • , A. Roy Thurik
    • , André G. Uitterlinden
    • , Jon White
    • , Harriet de Wit
    • , Jian Yang
    • , Lars Bertram
    • , Dorret I. Boomsma
    • , Tõnu Esko
    • , Ernst Fehr
    • , David A. Hinds
    • , Magnus Johannesson
    • , Meena Kumari
    • , David Laibson
    • , Patrik K. E. Magnusson
    • , Michelle N. Meyer
    • , Arcadi Navarro
    • , Abraham A. Palmer
    • , Tune H. Pers
    • , Danielle Posthuma
    • , Daniel Schunk
    • , Murray B. Stein
    • , Rauli Svento
    • , Henning Tiemeier
    • , Paul R. H. J. Timmers
    • , Patrick Turley
    • , Robert J. Ursano
    • , Gert G. Wagner
    • , James F. Wilson
    • , Jacob Gratten
    • , James J. Lee
    • , David Cesarini
    • , Daniel J. Benjamin
    • , Philipp D. Koellinger
    •  & Jonathan P. Beauchamp
  • Article |

    Genome-wide association analyses identify 301 new loci influencing bone mineral density and 13 loci influencing fracture risk. Integrative analyses of epigenomic data and mouse knockout phenotypes provide additional insights into osteoporosis pathophysiology.

    • John A. Morris
    • , John P. Kemp
    • , Scott E. Youlten
    • , Laetitia Laurent
    • , John G. Logan
    • , Ryan C. Chai
    • , Nicholas A. Vulpescu
    • , Vincenzo Forgetta
    • , Aaron Kleinman
    • , Sindhu T. Mohanty
    • , C. Marcelo Sergio
    • , Julian Quinn
    • , Loan Nguyen-Yamamoto
    • , Aimee-Lee Luco
    • , Jinchu Vijay
    • , Marie-Michelle Simon
    • , Albena Pramatarova
    • , Carolina Medina-Gomez
    • , Katerina Trajanoska
    • , Elena J. Ghirardello
    • , Natalie C. Butterfield
    • , Katharine F. Curry
    • , Victoria D. Leitch
    • , Penny C. Sparkes
    • , Anne-Tounsia Adoum
    • , Naila S. Mannan
    • , Davide S. K. Komla-Ebri
    • , Andrea S. Pollard
    • , Hannah F. Dewhurst
    • , Thomas A. D. Hassall
    • , Michael-John G. Beltejar
    • , Michelle Agee
    • , Babak Alipanahi
    • , Adam Auton
    • , Robert K. Bell
    • , Katarzyna Bryc
    • , Sarah L. Elson
    • , Pierre Fontanillas
    • , Nicholas A. Furlotte
    • , Jennifer C. McCreight
    • , Karen E. Huber
    • , Nadia K. Litterman
    • , Matthew H. McIntyre
    • , Joanna L. Mountain
    • , Elizabeth S. Noblin
    • , Carrie A. M. Northover
    • , Steven J. Pitts
    • , J. Fah Sathirapongsasuti
    • , Olga V. Sazonova
    • , Janie F. Shelton
    • , Suyash Shringarpure
    • , Chao Tian
    • , Joyce Y. Tung
    • , Vladimir Vacic
    • , Catherine H. Wilson
    • , Douglas J. Adams
    • , Suzanne M. Vaillancourt
    • , Stephen Kaptoge
    • , Paul Baldock
    • , Cyrus Cooper
    • , Jonathan Reeve
    • , Evangelia E. Ntzani
    • , Evangelos Evangelou
    • , Claes Ohlsson
    • , David Karasik
    • , Fernando Rivadeneira
    • , Douglas P. Kiel
    • , Jonathan H. Tobias
    • , Celia L. Gregson
    • , Nicholas C. Harvey
    • , Elin Grundberg
    • , David Goltzman
    • , David J. Adams
    • , Christopher J. Lelliott
    • , David A. Hinds
    • , Cheryl L. Ackert-Bicknell
    • , Yi-Hsiang Hsu
    • , Matthew T. Maurano
    • , Peter I. Croucher
    • , Graham R. Williams
    • , J. H. Duncan Bassett
    • , David M. Evans
    •  & J. Brent Richards
  • Article |

    Genome-wide-association analyses of datasets from Iceland and the UK identify risk variants for nasal polyps and chronic rhinosinusitis. Notably, a loss-of-function missense variant in ALOX15 confers protection against both phenotypes, thus identifying a potential target for therapeutic intervention.

    • Ragnar P. Kristjansson
    • , Stefania Benonisdottir
    • , Olafur B. Davidsson
    • , Asmundur Oddsson
    • , Vinicius Tragante
    • , Jon K. Sigurdsson
    • , Lilja Stefansdottir
    • , Stefan Jonsson
    • , Brynjar O. Jensson
    • , Joseph G. Arthur
    • , Gudny A. Arnadottir
    • , Gerald Sulem
    • , Bjarni V. Halldorsson
    • , Bjarni Gunnarsson
    • , Gisli H. Halldorsson
    • , Olafur A. Stefansson
    • , Gudjon R. Oskarsson
    • , Aimee M. Deaton
    • , Isleifur Olafsson
    • , Gudmundur I. Eyjolfsson
    • , Olof Sigurdardottir
    • , Pall T. Onundarson
    • , David Gislason
    • , Thorarinn Gislason
    • , Bjorn R. Ludviksson
    • , Dora Ludviksdottir
    • , Thorunn A. Olafsdottir
    • , Thorunn Rafnar
    • , Gisli Masson
    • , Florian Zink
    • , Gyda Bjornsdottir
    • , Olafur Th. Magnusson
    • , Unnur S. Bjornsdottir
    • , Gudmar Thorleifsson
    • , Gudmundur L. Norddahl
    • , Daniel F. Gudbjartsson
    • , Unnur Thorsteinsdottir
    • , Ingileif Jonsdottir
    • , Patrick Sulem
    •  & Kari Stefansson
  • Article |

    Analysis of 1,988 cases of B-cell acute lymphoblastic leukemia characterizes 23 subtypes defined by genomic features and shows that two of the subtypes have frequent PAX5 alterations.

    • Zhaohui Gu
    • , Michelle L. Churchman
    • , Kathryn G. Roberts
    • , Ian Moore
    • , Xin Zhou
    • , Joy Nakitandwe
    • , Kohei Hagiwara
    • , Stephane Pelletier
    • , Sebastien Gingras
    • , Hartmut Berns
    • , Debbie Payne-Turner
    • , Ashley Hill
    • , Ilaria Iacobucci
    • , Lei Shi
    • , Stanley Pounds
    • , Cheng Cheng
    • , Deqing Pei
    • , Chunxu Qu
    • , Scott Newman
    • , Meenakshi Devidas
    • , Yunfeng Dai
    • , Shalini C. Reshmi
    • , Julie Gastier-Foster
    • , Elizabeth A. Raetz
    • , Michael J. Borowitz
    • , Brent L. Wood
    • , William L. Carroll
    • , Patrick A. Zweidler-McKay
    • , Karen R. Rabin
    • , Leonard A. Mattano
    • , Kelly W. Maloney
    • , Alessandro Rambaldi
    • , Orietta Spinelli
    • , Jerald P. Radich
    • , Mark D. Minden
    • , Jacob M. Rowe
    • , Selina Luger
    • , Mark R. Litzow
    • , Martin S. Tallman
    • , Janis Racevskis
    • , Yanming Zhang
    • , Ravi Bhatia
    • , Jessica Kohlschmidt
    • , Krzysztof Mrózek
    • , Clara D. Bloomfield
    • , Wendy Stock
    • , Steven Kornblau
    • , Hagop M. Kantarjian
    • , Marina Konopleva
    • , Williams E. Evans
    • , Sima Jeha
    • , Ching-Hon Pui
    • , Jun Yang
    • , Elisabeth Paietta
    • , James R. Downing
    • , Mary V. Relling
    • , Jinghui Zhang
    • , Mignon L. Loh
    • , Stephen P. Hunger
    •  & Charles G. Mullighan
  • Article |

    Analysis of signatures of hypoxia in more than 8,000 tumors from 19 cancer types identifies hypoxia-driven mutation signatures and dysregulation of microRNAs.

    • Vinayak Bhandari
    • , Christianne Hoey
    • , Lydia Y. Liu
    • , Emilie Lalonde
    • , Jessica Ray
    • , Julie Livingstone
    • , Robert Lesurf
    • , Yu-Jia Shiah
    • , Tina Vujcic
    • , Xiaoyong Huang
    • , Shadrielle M. G. Espiritu
    • , Lawrence E. Heisler
    • , Fouad Yousif
    • , Vincent Huang
    • , Takafumi N. Yamaguchi
    • , Cindy Q. Yao
    • , Veronica Y. Sabelnykova
    • , Michael Fraser
    • , Melvin L. K. Chua
    • , Theodorus van der Kwast
    • , Stanley K. Liu
    • , Paul C. Boutros
    •  & Robert G. Bristow
  • Article |

    Analysis of genotyping-by-sequencing data for more than 20,000 barley accessions from a German genebank provides a framework for genomics-assisted genebank management and analysis of large germplasm collections for important crops.

    • Sara G. Milner
    • , Matthias Jost
    • , Shin Taketa
    • , Elena Rey Mazón
    • , Axel Himmelbach
    • , Markus Oppermann
    • , Stephan Weise
    • , Helmut Knüpffer
    • , Martín Basterrechea
    • , Patrick König
    • , Danuta Schüler
    • , Rajiv Sharma
    • , Raj K. Pasam
    • , Twan Rutten
    • , Ganggang Guo
    • , Dongdong Xu
    • , Jing Zhang
    • , Gerhard Herren
    • , Thomas Müller
    • , Simon G. Krattinger
    • , Beat Keller
    • , Yong Jiang
    • , Maria Y. González
    • , Yusheng Zhao
    • , Antje Habekuß
    • , Sandra Färber
    • , Frank Ordon
    • , Matthias Lange
    • , Andreas Börner
    • , Andreas Graner
    • , Jochen C. Reif
    • , Uwe Scholz
    • , Martin Mascher
    •  & Nils Stein

Analysis

Technical Reports

  • Technical Report |

    GARFIELD is a new approach that classifies genomic features related to phenotypes on the basis of integrating GWAS signals with functional annotations. GARFIELD is used to characterize enrichment patterns for 29 traits integrated with ENCODE and Roadmap Epigenomics annotations.

    • Valentina Iotchkova
    • , Graham R. S. Ritchie
    • , Matthias Geihs
    • , Sandro Morganella
    • , Josine L. Min
    • , Klaudia Walter
    • , Nicholas John Timpson
    • , Ian Dunham
    • , Ewan Birney
    •  & Nicole Soranzo
  • Technical Report |

    Graph Genome Pipeline is a read-alignment and variant-calling pipeline based on graph genomes that offers improved read-mapping and variant-calling accuracy while achieving speed comparable to those of linear reference genome pipelines.

    • Goran Rakocevic
    • , Vladimir Semenyuk
    • , Wan-Ping Lee
    • , James Spencer
    • , John Browning
    • , Ivan J. Johnson
    • , Vladan Arsenijevic
    • , Jelena Nadj
    • , Kaushik Ghose
    • , Maria C. Suciu
    • , Sun-Gou Ji
    • , Gülfem Demir
    • , Lizao Li
    • , Berke Ç. Toptaş
    • , Alexey Dolgoborodov
    • , Björn Pollex
    • , Iosif Spulber
    • , Irina Glotova
    • , Péter Kómár
    • , Andrew L. Stachyra
    • , Yilong Li
    • , Milos Popovic
    • , Morten Källberg
    • , Amit Jain
    •  & Deniz Kural

Amendments & Corrections

  • Author Correction |

    • Fredrick R. Schumacher
    • , Ali Amin Al Olama
    • , Sonja I. Berndt
    • , Sara Benlloch
    • , Mahbubl Ahmed
    • , Edward J. Saunders
    • , Tokhir Dadaev
    • , Daniel Leongamornlert
    • , Ezequiel Anokian
    • , Clara Cieza-Borrella
    • , Chee Goh
    • , Mark N. Brook
    • , Xin Sheng
    • , Laura Fachal
    • , Joe Dennis
    • , Jonathan Tyrer
    • , Kenneth Muir
    • , Artitaya Lophatananon
    • , Victoria L. Stevens
    • , Susan M. Gapstur
    • , Brian D. Carter
    • , Catherine M. Tangen
    • , Phyllis J. Goodman
    • , Ian M. Thompson Jr
    • , Jyotsna Batra
    • , Suzanne Chambers
    • , Leire Moya
    • , Judith Clements
    • , Lisa Horvath
    • , Wayne Tilley
    • , Gail P. Risbridger
    • , Henrik Gronberg
    • , Markus Aly
    • , Tobias Nordström
    • , Paul Pharoah
    • , Nora Pashayan
    • , Johanna Schleutker
    • , Teuvo L. J. Tammela
    • , Csilla Sipeky
    • , Anssi Auvinen
    • , Demetrius Albanes
    • , Stephanie Weinstein
    • , Alicja Wolk
    • , Niclas Håkansson
    • , Catharine M. L. West
    • , Alison M. Dunning
    • , Neil Burnet
    • , Lorelei A. Mucci
    • , Edward Giovannucci
    • , Gerald L. Andriole
    • , Olivier Cussenot
    • , Géraldine Cancel-Tassin
    • , Stella Koutros
    • , Laura E. Beane Freeman
    • , Karina Dalsgaard Sorensen
    • , Torben Falck Orntoft
    • , Michael Borre
    • , Lovise Maehle
    • , Eli Marie Grindedal
    • , David E. Neal
    • , Jenny L. Donovan
    • , Freddie C. Hamdy
    • , Richard M. Martin
    • , Ruth C. Travis
    • , Tim J. Key
    • , Robert J. Hamilton
    • , Neil E. Fleshner
    • , Antonio Finelli
    • , Sue Ann Ingles
    • , Mariana C. Stern
    • , Barry S. Rosenstein
    • , Sarah L. Kerns
    • , Harry Ostrer
    • , Yong-Jie Lu
    • , Hong-Wei Zhang
    • , Ninghan Feng
    • , Xueying Mao
    • , Xin Guo
    • , Guomin Wang
    • , Zan Sun
    • , Graham G. Giles
    • , Melissa C. Southey
    • , Robert J. MacInnis
    • , Liesel M. FitzGerald
    • , Adam S. Kibel
    • , Bettina F. Drake
    • , Ana Vega
    • , Antonio Gómez-Caamaño
    • , Robert Szulkin
    • , Martin Eklund
    • , Manolis Kogevinas
    • , Javier Llorca
    • , Gemma Castaño-Vinyals
    • , Kathryn L. Penney
    • , Meir Stampfer
    • , Jong Y. Park
    • , Thomas A. Sellers
    • , Hui-Yi Lin
    • , Janet L. Stanford
    • , Cezary Cybulski
    • , Dominika Wokolorczyk
    • , Jan Lubinski
    • , Elaine A. Ostrander
    • , Milan S. Geybels
    • , Børge G. Nordestgaard
    • , Sune F. Nielsen
    • , Maren Weischer
    • , Rasmus Bisbjerg
    • , Martin Andreas Røder
    • , Peter Iversen
    • , Hermann Brenner
    • , Katarina Cuk
    • , Bernd Holleczek
    • , Christiane Maier
    • , Manuel Luedeke
    • , Thomas Schnoeller
    • , Jeri Kim
    • , Christopher J. Logothetis
    • , Esther M. John
    • , Manuel R. Teixeira
    • , Paula Paulo
    • , Marta Cardoso
    • , Susan L. Neuhausen
    • , Linda Steele
    • , Yuan Chun Ding
    • , Kim De Ruyck
    • , Gert De Meerleer
    • , Piet Ost
    • , Azad Razack
    • , Jasmine Lim
    • , Soo-Hwang Teo
    • , Daniel W. Lin
    • , Lisa F. Newcomb
    • , Davor Lessel
    • , Marija Gamulin
    • , Tomislav Kulis
    • , Radka Kaneva
    • , Nawaid Usmani
    • , Sandeep Singhal
    • , Chavdar Slavov
    • , Vanio Mitev
    • , Matthew Parliament
    • , Frank Claessens
    • , Steven Joniau
    • , Thomas Van den Broeck
    • , Samantha Larkin
    • , Paul A. Townsend
    • , Claire Aukim-Hastie
    • , Manuela Gago-Dominguez
    • , Jose Esteban Castelao
    • , Maria Elena Martinez
    • , Monique J. Roobol
    • , Guido Jenster
    • , Ron H. N. van Schaik
    • , Florence Menegaux
    • , Thérèse Truong
    • , Yves Akoli Koudou
    • , Jianfeng Xu
    • , Kay-Tee Khaw
    • , Lisa Cannon-Albright
    • , Hardev Pandha
    • , Agnieszka Michael
    • , Stephen N. Thibodeau
    • , Shannon K. McDonnell
    • , Daniel J. Schaid
    • , Sara Lindstrom
    • , Constance Turman
    • , Jing Ma
    • , David J. Hunter
    • , Elio Riboli
    • , Afshan Siddiq
    • , Federico Canzian
    • , Laurence N. Kolonel
    • , Loic Le Marchand
    • , Robert N. Hoover
    • , Mitchell J. Machiela
    • , Zuxi Cui
    • , Peter Kraft
    • , Christopher I. Amos
    • , David V. Conti
    • , Douglas F. Easton
    • , Fredrik Wiklund
    • , Stephen J. Chanock
    • , Brian E. Henderson
    • , Zsofia Kote-Jarai
    • , Christopher A. Haiman
    •  & Rosalind A. Eeles
  • Author Correction |

    • Rachel M. Sherman
    • , Juliet Forman
    • , Valentin Antonescu
    • , Daniela Puiu
    • , Michelle Daya
    • , Nicholas Rafaels
    • , Meher Preethi Boorgula
    • , Sameer Chavan
    • , Candelaria Vergara
    • , Victor E. Ortega
    • , Albert M. Levin
    • , Celeste Eng
    • , Maria Yazdanbakhsh
    • , James G. Wilson
    • , Javier Marrugo
    • , Leslie A. Lange
    • , L. Keoki Williams
    • , Harold Watson
    • , Lorraine B. Ware
    • , Christopher O. Olopade
    • , Olufunmilayo Olopade
    • , Ricardo R. Oliveira
    • , Carole Ober
    • , Dan L. Nicolae
    • , Deborah A. Meyers
    • , Alvaro Mayorga
    • , Jennifer Knight-Madden
    • , Tina Hartert
    • , Nadia N. Hansel
    • , Marilyn G. Foreman
    • , Jean G. Ford
    • , Mezbah U. Faruque
    • , Georgia M. Dunston
    • , Luis Caraballo
    • , Esteban G. Burchard
    • , Eugene R. Bleecker
    • , Maria I. Araujo
    • , Edwin F. Herrera-Paz
    • , Monica Campbell
    • , Cassandra Foster
    • , Margaret A. Taub
    • , Terri H. Beaty
    • , Ingo Ruczinski
    • , Rasika A. Mathias
    • , Kathleen C. Barnes
    •  & Steven L. Salzberg