Volume 51 Issue 4, April 2019

Volume 51 Issue 4

Torn canvas

This image depicts a key step in the discovery of a repeat expansion in RFC1 as a common cause of a late-onset ataxia syndrome known as CANVAS. A visual break in the sequence alignment, depicted here as a torn canvas, is produced by unjoined reads originating on each side of the expansion, disrupting the otherwise continuous tiling pattern.

See Cortese et al.

Image: Artwork by Simone Antonello and Andrea Cortese. Cover Design: Erin Dewalt.

Editorial

  • Editorial |

    Genetic resources and analyses overwhelmingly center on individuals of European ancestry. We encourage the community to embrace a global approach to genetic and genomic studies to address imbalances in the composition of cohorts and the subsequent translatability of findings.

News & Views

  • News & Views |

    More than one dozen hereditary ataxias are caused by repeat expansions. A newly discovered expansion may be the first known common genetic cause of late-onset ataxia.

    • Vikram Shakkottai
    •  & Henry Paulson
  • News & Views |

    Resolving variant-to-function relationships is a key challenge faced by human geneticists. A new study combining statistical fine-mapping with cell-type-specific functional annotations advances the understanding of the regulatory consequences of genetic variants associated with variations in blood-cell traits.

    • Manuel Tardaguila
    •  & Nicole Soranzo

Perspectives

  • Perspective |

    This Perspective discusses scientific and ethical considerations regarding the clinical use of polygenic risk scores, highlighting the pressing need to diversify cohorts for genetic studies beyond European-ancestry populations.

    • Alicia R. Martin
    • , Masahiro Kanai
    • , Yoichiro Kamatani
    • , Yukinori Okada
    • , Benjamin M. Neale
    •  & Mark J. Daly
  • Perspective |

    Transcriptome-wide association studies (TWAS) prioritize candidate causal genes at GWAS loci. This Perspective discusses the challenges to TWAS analysis, caveats to interpretation of results and opportunities for improvements to this class of methods.

    • Michael Wainberg
    • , Nasa Sinnott-Armstrong
    • , Nicholas Mancuso
    • , Alvaro N. Barbeira
    • , David A. Knowles
    • , David Golan
    • , Raili Ermel
    • , Arno Ruusalepp
    • , Thomas Quertermous
    • , Ke Hao
    • , Johan L. M. Björkegren
    • , Hae Kyung Im
    • , Bogdan Pasaniuc
    • , Manuel A. Rivas
    •  & Anshul Kundaje

Letters

  • Letter |

    Mendelian randomization analyses using genotyping data, gut metagenomic sequence and fecal short-chain-fatty-acid levels from 952 individuals combined with GWAS data show evidence of a causal effect of the gut microbiome on metabolic traits.

    • Serena Sanna
    • , Natalie R. van Zuydam
    • , Anubha Mahajan
    • , Alexander Kurilshikov
    • , Arnau Vich Vila
    • , Urmo Võsa
    • , Zlatan Mujagic
    • , Ad A. M. Masclee
    • , Daisy M. A. E. Jonkers
    • , Marije Oosting
    • , Leo A. B. Joosten
    • , Mihai G. Netea
    • , Lude Franke
    • , Alexandra Zhernakova
    • , Jingyuan Fu
    • , Cisca Wijmenga
    •  & Mark I. McCarthy
  • Letter |

    The authors transcriptionally profiled postmortem retinas from 453 age-related macular degeneration (AMD) cases and controls. Integration of AMD GWAS with eQTL analysis and TWAS identified several AMD-associated genes.

    • Rinki Ratnapriya
    • , Olukayode A. Sosina
    • , Margaret R. Starostik
    • , Madeline Kwicklis
    • , Rebecca J. Kapphahn
    • , Lars G. Fritsche
    • , Ashley Walton
    • , Marios Arvanitis
    • , Linn Gieser
    • , Alexandra Pietraszkiewicz
    • , Sandra R. Montezuma
    • , Emily Y. Chew
    • , Alexis Battle
    • , Gonçalo R. Abecasis
    • , Deborah A. Ferrington
    • , Nilanjan Chatterjee
    •  & Anand Swaroop
  • Letter |

    A pan-cancer analysis identifies 129 transposable-element-driven promoter-activation events involving 106 oncogenes. At the AluJb-LIN28B locus, deletion of the transposable element eliminates oncogene expression.

    • Hyo Sik Jang
    • , Nakul M. Shah
    • , Alan Y. Du
    • , Zea Z. Dailey
    • , Erica C. Pehrsson
    • , Paula M. Godoy
    • , David Zhang
    • , Daofeng Li
    • , Xiaoyun Xing
    • , Sungsu Kim
    • , David O’Donnell
    • , Jeffrey I. Gordon
    •  & Ting Wang
  • Letter |

    This study uses SMARCA2/4-mutant variants to define catalytic activity–dependent and catalytic activity–independent contributions of the ATPase module to the targeting of BAF and PBAF complexes genome-wide.

    • Joshua Pan
    • , Zachary M. McKenzie
    • , Andrew R. D’Avino
    • , Nazar Mashtalir
    • , Caleb A. Lareau
    • , Roodolph St. Pierre
    • , Lu Wang
    • , Ali Shilatifard
    •  & Cigall Kadoch
  • Letter |

    Generation of a library of 62,389 mapped insertion mutants for the unicellular alga Chlamydomonas reinhardtii enables screening for genes required for photosynthesis and the identification of 303 candidate genes.

    • Xiaobo Li
    • , Weronika Patena
    • , Friedrich Fauser
    • , Robert E. Jinkerson
    • , Shai Saroussi
    • , Moritz T. Meyer
    • , Nina Ivanova
    • , Jacob M. Robertson
    • , Rebecca Yue
    • , Ru Zhang
    • , Josep Vilarrasa-Blasi
    • , Tyler M. Wittkopp
    • , Silvia Ramundo
    • , Sean R. Blum
    • , Audrey Goh
    • , Matthew Laudon
    • , Tharan Srikumar
    • , Paul A. Lefebvre
    • , Arthur R. Grossman
    •  & Martin C. Jonikas

Articles

  • Article |

    A multi-ancestry genome-wide gene–smoking interaction study identifies 13 new loci associated with serum lipids.

    • Amy R. Bentley
    • , Yun J. Sung
    • , Michael R. Brown
    • , Thomas W. Winkler
    • , Aldi T. Kraja
    • , Ioanna Ntalla
    • , Karen Schwander
    • , Daniel I. Chasman
    • , Elise Lim
    • , Xuan Deng
    • , Xiuqing Guo
    • , Jingmin Liu
    • , Yingchang Lu
    • , Ching-Yu Cheng
    • , Xueling Sim
    • , Dina Vojinovic
    • , Jennifer E. Huffman
    • , Solomon K. Musani
    • , Changwei Li
    • , Mary F. Feitosa
    • , Melissa A. Richard
    • , Raymond Noordam
    • , Jenna Baker
    • , Guanjie Chen
    • , Hugues Aschard
    • , Traci M. Bartz
    • , Jingzhong Ding
    • , Rajkumar Dorajoo
    • , Alisa K. Manning
    • , Tuomo Rankinen
    • , Albert V. Smith
    • , Salman M. Tajuddin
    • , Wei Zhao
    • , Mariaelisa Graff
    • , Maris Alver
    • , Mathilde Boissel
    • , Jin Fang Chai
    • , Xu Chen
    • , Jasmin Divers
    • , Evangelos Evangelou
    • , Chuan Gao
    • , Anuj Goel
    • , Yanick Hagemeijer
    • , Sarah E. Harris
    • , Fernando P. Hartwig
    • , Meian He
    • , Andrea R. V. R. Horimoto
    • , Fang-Chi Hsu
    • , Yi-Jen Hung
    • , Anne U. Jackson
    • , Anuradhani Kasturiratne
    • , Pirjo Komulainen
    • , Brigitte Kühnel
    • , Karin Leander
    • , Keng-Hung Lin
    • , Jian’an Luan
    • , Leo-Pekka Lyytikäinen
    • , Nana Matoba
    • , Ilja M. Nolte
    • , Maik Pietzner
    • , Bram Prins
    • , Muhammad Riaz
    • , Antonietta Robino
    • , M. Abdullah Said
    • , Nicole Schupf
    • , Robert A. Scott
    • , Tamar Sofer
    • , Alena Stancáková
    • , Fumihiko Takeuchi
    • , Bamidele O. Tayo
    • , Peter J. van der Most
    • , Tibor V. Varga
    • , Tzung-Dau Wang
    • , Yajuan Wang
    • , Erin B. Ware
    • , Wanqing Wen
    • , Yong-Bing Xiang
    • , Lisa R. Yanek
    • , Weihua Zhang
    • , Jing Hua Zhao
    • , Adebowale Adeyemo
    • , Saima Afaq
    • , Najaf Amin
    • , Marzyeh Amini
    • , Dan E. Arking
    • , Zorayr Arzumanyan
    • , Tin Aung
    • , Christie Ballantyne
    • , R. Graham Barr
    • , Lawrence F. Bielak
    • , Eric Boerwinkle
    • , Erwin P. Bottinger
    • , Ulrich Broeckel
    • , Morris Brown
    • , Brian E. Cade
    • , Archie Campbell
    • , Mickaël Canouil
    • , Sabanayagam Charumathi
    • , Yii-Der Ida Chen
    • , Kaare Christensen
    • , Maria Pina Concas
    • , John M. Connell
    • , Lisa de las Fuentes
    • , H. Janaka de Silva
    • , Paul S. de Vries
    • , Ayo Doumatey
    • , Qing Duan
    • , Charles B. Eaton
    • , Ruben N. Eppinga
    • , Jessica D. Faul
    • , James S. Floyd
    • , Nita G. Forouhi
    • , Terrence Forrester
    • , Yechiel Friedlander
    • , Ilaria Gandin
    • , He Gao
    • , Mohsen Ghanbari
    • , Sina A. Gharib
    • , Bruna Gigante
    • , Franco Giulianini
    • , Hans J. Grabe
    • , C. Charles Gu
    • , Tamara B. Harris
    • , Sami Heikkinen
    • , Chew-Kiat Heng
    • , Makoto Hirata
    • , James E. Hixson
    • , M. Arfan Ikram
    • , Yucheng Jia
    • , Roby Joehanes
    • , Craig Johnson
    • , Jost Bruno Jonas
    • , Anne E. Justice
    • , Tomohiro Katsuya
    • , Chiea Chuen Khor
    • , Tuomas O. Kilpeläinen
    • , Woon-Puay Koh
    • , Ivana Kolcic
    • , Charles Kooperberg
    • , Jose E. Krieger
    • , Stephen B. Kritchevsky
    • , Michiaki Kubo
    • , Johanna Kuusisto
    • , Timo A. Lakka
    • , Carl D. Langefeld
    • , Claudia Langenberg
    • , Lenore J. Launer
    • , Benjamin Lehne
    • , Cora E. Lewis
    • , Yize Li
    • , Jingjing Liang
    • , Shiow Lin
    • , Ching-Ti Liu
    • , Jianjun Liu
    • , Kiang Liu
    • , Marie Loh
    • , Kurt K. Lohman
    • , Tin Louie
    • , Anna Luzzi
    • , Reedik Mägi
    • , Anubha Mahajan
    • , Ani W. Manichaikul
    • , Colin A. McKenzie
    • , Thomas Meitinger
    • , Andres Metspalu
    • , Yuri Milaneschi
    • , Lili Milani
    • , Karen L. Mohlke
    • , Yukihide Momozawa
    • , Andrew P. Morris
    • , Alison D. Murray
    • , Mike A. Nalls
    • , Matthias Nauck
    • , Christopher P. Nelson
    • , Kari E. North
    • , Jeffrey R. O’Connell
    • , Nicholette D. Palmer
    • , George J. Papanicolau
    • , Nancy L. Pedersen
    • , Annette Peters
    • , Patricia A. Peyser
    • , Ozren Polasek
    • , Neil Poulter
    • , Olli T. Raitakari
    • , Alex P. Reiner
    • , Frida Renström
    • , Treva K. Rice
    • , Stephen S. Rich
    • , Jennifer G. Robinson
    • , Lynda M. Rose
    • , Frits R. Rosendaal
    • , Igor Rudan
    • , Carsten O. Schmidt
    • , Pamela J. Schreiner
    • , William R. Scott
    • , Peter Sever
    • , Yuan Shi
    • , Stephen Sidney
    • , Mario Sims
    • , Jennifer A. Smith
    • , Harold Snieder
    • , John M. Starr
    • , Konstantin Strauch
    • , Heather M. Stringham
    • , Nicholas Y. Q. Tan
    • , Hua Tang
    • , Kent D. Taylor
    • , Yik Ying Teo
    • , Yih Chung Tham
    • , Henning Tiemeier
    • , Stephen T. Turner
    • , André G. Uitterlinden
    • , Diana van Heemst
    • , Melanie Waldenberger
    • , Heming Wang
    • , Lan Wang
    • , Lihua Wang
    • , Wen Bin Wei
    • , Christine A. Williams
    • , Gregory Wilson Sr
    • , Mary K. Wojczynski
    • , Jie Yao
    • , Kristin Young
    • , Caizheng Yu
    • , Jian-Min Yuan
    • , Jie Zhou
    • , Alan B. Zonderman
    • , Diane M. Becker
    • , Michael Boehnke
    • , Donald W. Bowden
    • , John C. Chambers
    • , Richard S. Cooper
    • , Ulf de Faire
    • , Ian J. Deary
    • , Paul Elliott
    • , Tõnu Esko
    • , Martin Farrall
    • , Paul W. Franks
    • , Barry I. Freedman
    • , Philippe Froguel
    • , Paolo Gasparini
    • , Christian Gieger
    • , Bernardo L. Horta
    • , Jyh-Ming Jimmy Juang
    • , Yoichiro Kamatani
    • , Candace M. Kammerer
    • , Norihiro Kato
    • , Jaspal S. Kooner
    • , Markku Laakso
    • , Cathy C. Laurie
    • , I-Te Lee
    • , Terho Lehtimäki
    • , Patrik K. E. Magnusson
    • , Albertine J. Oldehinkel
    • , Brenda W. J. H. Penninx
    • , Alexandre C. Pereira
    • , Rainer Rauramaa
    • , Susan Redline
    • , Nilesh J. Samani
    • , James Scott
    • , Xiao-Ou Shu
    • , Pim van der Harst
    • , Lynne E. Wagenknecht
    • , Jun-Sing Wang
    • , Ya Xing Wang
    • , Nicholas J. Wareham
    • , Hugh Watkins
    • , David R. Weir
    • , Ananda R. Wickremasinghe
    • , Tangchun Wu
    • , Eleftheria Zeggini
    • , Wei Zheng
    • , Claude Bouchard
    • , Michele K. Evans
    • , Vilmundur Gudnason
    • , Sharon L. R. Kardia
    • , Yongmei Liu
    • , Bruce M. Psaty
    • , Paul M. Ridker
    • , Rob M. van Dam
    • , Dennis O. Mook-Kanamori
    • , Myriam Fornage
    • , Michael A. Province
    • , Tanika N. Kelly
    • , Ervin R. Fox
    • , Caroline Hayward
    • , Cornelia M. van Duijn
    • , E. Shyong Tai
    • , Tien Yin Wong
    • , Ruth J. F. Loos
    • , Nora Franceschini
    • , Jerome I. Rotter
    • , Xiaofeng Zhu
    • , Laura J. Bierut
    • , W. James Gauderman
    • , Kenneth Rice
    • , Patricia B. Munroe
    • , Alanna C. Morrison
    • , Dabeeru C. Rao
    • , Charles N. Rotimi
    •  & L. Adrienne Cupples
  • Article |

    Biallelic expansion of an intronic AAGGG repeat in RFC1 is identified here as a common cause of late-onset ataxia. This expansion occurs in the poly(A) tail of an AluSx3 element and is observed at a carrier frequency of 0.7% in populations of European ancestry.

    • Andrea Cortese
    • , Roberto Simone
    • , Roisin Sullivan
    • , Jana Vandrovcova
    • , Huma Tariq
    • , Wai Yan Yau
    • , Jack Humphrey
    • , Zane Jaunmuktane
    • , Prasanth Sivakumar
    • , James Polke
    • , Muhammad Ilyas
    • , Eloise Tribollet
    • , Pedro J. Tomaselli
    • , Grazia Devigili
    • , Ilaria Callegari
    • , Maurizio Versino
    • , Vincenzo Salpietro
    • , Stephanie Efthymiou
    • , Diego Kaski
    • , Nick W. Wood
    • , Nadja S. Andrade
    • , Elena Buglo
    • , Adriana Rebelo
    • , Alexander M. Rossor
    • , Adolfo Bronstein
    • , Pietro Fratta
    • , Wilson J. Marques
    • , Stephan Züchner
    • , Mary M. Reilly
    •  & Henry Houlden
  • Article |

    This study uses gene expression predictors for the dorsolateral prefrontal cortex and other brain regions to perform a transcriptomic imputation analysis of schizophrenia, identifying 413 genic associations across 13 brain regions and 36 significantly enriched pathways.

    • Laura M. Huckins
    • , Amanda Dobbyn
    • , Douglas M. Ruderfer
    • , Gabriel Hoffman
    • , Weiqing Wang
    • , Antonio F. Pardiñas
    • , Veera M. Rajagopal
    • , Thomas D. Als
    • , Hoang T. Nguyen
    • , Kiran Girdhar
    • , James Boocock
    • , Panos Roussos
    • , Menachem Fromer
    • , Robin Kramer
    • , Enrico Domenici
    • , Eric R. Gamazon
    • , Shaun Purcell
    • , Jessica S. Johnson
    • , Hardik R. Shah
    • , Lambertus L. Klein
    • , Kristen K. Dang
    • , Benjamin A. Logsdon
    • , Milind C. Mahajan
    • , Lara M. Mangravite
    • , Hiroyoshi Toyoshiba
    • , Raquel E. Gur
    • , Chang-Gyu Hahn
    • , Eric Schadt
    • , David A. Lewis
    • , Vahram Haroutunian
    • , Mette A. Peters
    • , Barbara K. Lipska
    • , Joseph D. Buxbaum
    • , Keisuke Hirai
    • , Thanneer M. Perumal
    • , Laurent Essioux
    • , Stephan Ripke
    • , Benjamin M. Neale
    • , Aiden Corvin
    • , James T. R. Walters
    • , Kai-How Farh
    • , Peter A. Holmans
    • , Phil Lee
    • , Brendan Bulik-Sullivan
    • , David A. Collier
    • , Hailiang Huang
    • , Tune H. Pers
    • , Ingrid Agartz
    • , Esben Agerbo
    • , Margot Albus
    • , Madeline Alexander
    • , Farooq Amin
    • , Silviu A. Bacanu
    • , Martin Begemann
    • , Richard A. Belliveau Jr
    • , Judit Bene
    • , Sarah E. Bergen
    • , Elizabeth Bevilacqua
    • , Tim B. Bigdeli
    • , Donald W. Black
    • , Richard Bruggeman
    • , Nancy G. Buccola
    • , Randy L. Buckner
    • , William Byerley
    • , Wiepke Cahn
    • , Guiqing Cai
    • , Dominique Campion
    • , Rita M. Cantor
    • , Vaughan J. Carr
    • , Noa Carrera
    • , Stanley V. Catts
    • , Kimberly D. Chambert
    • , Raymond C. K. Chan
    • , Ronald Y. L. Chen
    • , Eric Y. H. Chen
    • , Wei Cheng
    • , Eric F. C. Cheung
    • , Siow Ann Chong
    • , C. Robert Cloninger
    • , David Cohen
    • , Nadine Cohen
    • , Paul Cormican
    • , Nick Craddock
    • , James J. Crowley
    • , David Curtis
    • , Michael Davidson
    • , Kenneth L. Davis
    • , Franziska Degenhardt
    • , Jurgen Del Favero
    • , Ditte Demontis
    • , Dimitris Dikeos
    • , Timothy Dinan
    • , Srdjan Djurovic
    • , Gary Donohoe
    • , Elodie Drapeau
    • , Jubao Duan
    • , Frank Dudbridge
    • , Naser Durmishi
    • , Peter Eichhammer
    • , Johan Eriksson
    • , Valentina Escott-Price
    • , Laurent Essioux
    • , Ayman H. Fanous
    • , Martilias S. Farrell
    • , Josef Frank
    • , Lude Franke
    • , Robert Freedman
    • , Nelson B. Freimer
    • , Marion Friedl
    • , Joseph I. Friedman
    • , Menachem Fromer
    • , Giulio Genovese
    • , Lyudmila Georgieva
    • , Ina Giegling
    • , Paola Giusti-Rodríguez
    • , Stephanie Godard
    • , Jacqueline I. Goldstein
    • , Vera Golimbet
    • , Srihari Gopal
    • , Jacob Gratten
    • , Lieuwe de Haan
    • , Christian Hammer
    • , Marian L. Hamshere
    • , Mark Hansen
    • , Thomas Hansen
    • , Vahram Haroutunian
    • , Annette M. Hartmann
    • , Frans A. Henskens
    • , Stefan Herms
    • , Joel N. Hirschhorn
    • , Per Hoffmann
    • , Andrea Hofman
    • , Mads V. Hollegaard
    • , David M. Hougaard
    • , Masashi Ikeda
    • , Inge Joa
    • , Antonio Julia
    • , Rene S. Kahn
    • , Luba Kalaydjieva
    • , Sena Karachanak-Yankova
    • , Juha Karjalainen
    • , David Kavanagh
    • , Matthew C. Keller
    • , James L. Kennedy
    • , Andrey Khrunin
    • , Yunjung Kim
    • , Janis Klovins
    • , James A. Knowles
    • , Bettina Konte
    • , Vaidutis Kucinskas
    • , Zita Ausrele Kucinskiene
    • , Hana Kuzelova-Ptackova
    • , Anna K. Kahler
    • , Claudine Laurent
    • , Jimmy Lee Chee Keong
    • , S. Hong Lee
    • , Sophie E. Legge
    • , Bernard Lerer
    • , Miaoxin Li
    • , Tao Li
    • , Kung-Yee Liang
    • , Jeffrey Lieberman
    • , Svetlana Limborska
    • , Carmel M. Loughland
    • , Jan Lubinski
    • , Jouko Lonnqvist
    • , Milan Macek Jr
    • , Patrik K. E. Magnusson
    • , Brion S. Maher
    • , Wolfgang Maier
    • , Jacques Mallet
    • , Sara Marsal
    • , Manuel Mattheisen
    • , Morten Mattingsdal
    • , Robert W. McCarley
    • , Colm McDonald
    • , Andrew M. McIntosh
    • , Sandra Meier
    • , Carin J. Meijer
    • , Bela Melegh
    • , Ingrid Melle
    • , Raquelle I. Mesholam-Gately
    • , Andres Metspalu
    • , Patricia T. Michie
    • , Lili Milani
    • , Vihra Milanova
    • , Younes Mokrab
    • , Derek W. Morris
    • , Ole Mors
    • , Kieran C. Murphy
    • , Robin M. Murray
    • , Inez Myin-Germeys
    • , Bertram Muller-Myhsok
    • , Mari Nelis
    • , Igor Nenadic
    • , Deborah A. Nertney
    • , Gerald Nestadt
    • , Kristin K. Nicodemus
    • , Liene Nikitina-Zake
    • , Laura Nisenbaum
    • , Annelie Nordin
    • , Eadbhard O’Callaghan
    • , Colm O’Dushlaine
    • , F. Anthony O’Neill
    • , Sang-Yun Oh
    • , Ann Olincy
    • , Line Olsen
    • , Jim Van Os
    • , Christos Pantelis
    • , George N. Papadimitriou
    • , Sergi Papiol
    • , Elena Parkhomenko
    • , Michele T. Pato
    • , Tiina Paunio
    • , Milica Pejovic-Milovancevic
    • , Diana O. Perkins
    • , Olli Pietiläinen
    • , Jonathan Pimm
    • , Andrew J. Pocklington
    • , John Powell
    • , Alkes Price
    • , Ann E. Pulver
    • , Shaun M. Purcell
    • , Digby Quested
    • , Henrik B. Rasmussen
    • , Abraham Reichenberg
    • , Mark A. Reimers
    • , Alexander L. Richards
    • , Joshua L. Roffman
    • , Panos Roussos
    • , Douglas M. Ruderfer
    • , Veikko Salomaa
    • , Alan R. Sanders
    • , Ulrich Schall
    • , Christian R. Schubert
    • , Thomas G. Schulze
    • , Sibylle G. Schwab
    • , Edward M. Scolnick
    • , Rodney J. Scott
    • , Larry J. Seidman
    • , Jianxin Shi
    • , Engilbert Sigurdsson
    • , Teimuraz Silagadze
    • , Jeremy M. Silverman
    • , Kang Sim
    • , Petr Slominsky
    • , Jordan W. Smoller
    • , Hon-Cheong So
    • , Chris C. A. Spencer
    • , Eli A. Stahl
    • , Hreinn Stefansson
    • , Stacy Steinberg
    • , Elisabeth Stogmann
    • , Richard E. Straub
    • , Eric Strengman
    • , Jana Strohmaier
    • , T. Scott Stroup
    • , Mythily Subramaniam
    • , Jaana Suvisaari
    • , Dragan M. Svrakic
    • , Jin P. Szatkiewicz
    • , Erik Soderman
    • , Srinivas Thirumalai
    • , Draga Toncheva
    • , Sarah Tosato
    • , Juha Veijola
    • , John Waddington
    • , Dermot Walsh
    • , Dai Wang
    • , Qiang Wang
    • , Bradley T. Webb
    • , Mark Weiser
    • , Dieter B. Wildenauer
    • , Nigel M. Williams
    • , Stephanie Williams
    • , Stephanie H. Witt
    • , Aaron R. Wolen
    • , Emily H. M. Wong
    • , Brandon K. Wormley
    • , Hualin Simon Xi
    • , Clement C. Zai
    • , Xuebin Zheng
    • , Fritz Zimprich
    • , Naomi R. Wray
    • , Kari Stefansson
    • , Peter M. Visscher
    • , Rolf Adolfsson
    • , Ole A. Andreassen
    • , Douglas H. R. Blackwood
    • , Elvira Bramon
    • , Joseph D. Buxbaum
    • , Anders D. Børglum
    • , Sven Cichon
    • , Ariel Darvasi
    • , Enrico Domenici
    • , Hannelore Ehrenreich
    • , Tonu Esko
    • , Pablo V. Gejman
    • , Michael Gill
    • , Hugh Gurling
    • , Christina M. Hultman
    • , Nakao Iwata
    • , Assen V. Jablensky
    • , Erik G. Jonsson
    • , Kenneth S. Kendler
    • , George Kirov
    • , Jo Knight
    • , Todd Lencz
    • , Douglas F. Levinson
    • , Qingqin S. Li
    • , Jianjun Liu
    • , Anil K. Malhotra
    • , Steven A. McCarroll
    • , Andrew McQuillin
    • , Jennifer L. Moran
    • , Preben B. Mortensen
    • , Bryan J. Mowry
    • , Markus M. Nothen
    • , Roel A. Ophoff
    • , Michael J. Owen
    • , Aarno Palotie
    • , Carlos N. Pato
    • , Tracey L. Petryshen
    • , Danielle Posthuma
    • , Marcella Rietschel
    • , Brien P. Riley
    • , Dan Rujescu
    • , Pak C. Sham
    • , Pamela Sklar
    • , David St Clair
    • , Daniel R. Weinberger
    • , Jens R. Wendland
    • , Thomas Werge
    • , Mark J. Daly
    • , Patrick F. Sullivan
    • , Michael C. O’Donovan
    • , Anders D. Børglum
    • , Ditte Demontis
    • , Veera Manikandan Rajagopal
    • , Thomas D. Als
    • , Manuel Mattheisen
    • , Jakob Grove
    • , Thomas Werge
    • , Preben Bo Mortensen
    • , Carsten Bøcker Pedersen
    • , Esben Agerbo
    • , Marianne Giørtz Pedersen
    • , Ole Mors
    • , Merete Nordentoft
    • , David M. Hougaard
    • , Jonas Bybjerg-Grauholm
    • , Marie Bækvad-Hansen
    • , Christine Søholm Hansen
    • , Ditte Demontis
    • , Anders D. Børglum
    • , James T. R. Walters
    • , Michael C. O’Donovan
    • , Patrick Sullivan
    • , Michael J. Owen
    • , Bernie Devlin
    • , Solveig K. Sieberts
    • , Nancy J. Cox
    • , Hae Kyung Im
    • , Pamela Sklar
    •  & Eli A. Stahl
  • Article |

    FOCUS (fine-mapping of causal gene sets) models correlation among TWAS signals to assign a probability for every gene in the risk region to explain the observed association signal while controlling for pleiotropic SNP effects and unmeasured causal expression.

    • Nicholas Mancuso
    • , Malika K. Freund
    • , Ruth Johnson
    • , Huwenbo Shi
    • , Gleb Kichaev
    • , Alexander Gusev
    •  & Bogdan Pasaniuc
  • Article |

    Fine-mapping of blood cell traits in the UK Biobank identifies putative causal variants and enrichment of fine-mapped variants in accessible chromatin of hematopoietic progenitor cells. The study provides an analytical framework for single-variant and single-cell analyses of genetic associations.

    • Jacob C. Ulirsch
    • , Caleb A. Lareau
    • , Erik L. Bao
    • , Leif S. Ludwig
    • , Michael H. Guo
    • , Christian Benner
    • , Ansuman T. Satpathy
    • , Vinay K. Kartha
    • , Rany M. Salem
    • , Joel N. Hirschhorn
    • , Hilary K. Finucane
    • , Martin J. Aryee
    • , Jason D. Buenrostro
    •  & Vijay G. Sankaran
  • Article |

    Analysis of genomic and clinical features of acute erythroid leukemia in comparison to other myeloid disorders supports its distinct classification, defines subgroups and suggests therapeutic vulnerabilities.

    • Ilaria Iacobucci
    • , Ji Wen
    • , Manja Meggendorfer
    • , John K. Choi
    • , Lei Shi
    • , Stanley B. Pounds
    • , Catherine L. Carmichael
    • , Katherine E. Masih
    • , Sarah M. Morris
    • , R. Coleman Lindsley
    • , Laura J. Janke
    • , Thomas B. Alexander
    • , Guangchun Song
    • , Chunxu Qu
    • , Yongjin Li
    • , Debbie Payne-Turner
    • , Daisuke Tomizawa
    • , Nobutaka Kiyokawa
    • , Marcus Valentine
    • , Virginia Valentine
    • , Giuseppe Basso
    • , Franco Locatelli
    • , Eric J. Enemark
    • , Shirley K. Y. Kham
    • , Allen E. J. Yeoh
    • , Xiaotu Ma
    • , Xin Zhou
    • , Edgar Sioson
    • , Michael Rusch
    • , Rhonda E. Ries
    • , Elliot Stieglitz
    • , Stephen P. Hunger
    • , Andrew H. Wei
    • , L Bik To
    • , Ian D. Lewis
    • , Richard J. D’Andrea
    • , Benjamin T. Kile
    • , Anna L. Brown
    • , Hamish S. Scott
    • , Christopher N. Hahn
    • , Paula Marlton
    • , Deqing Pei
    • , Cheng Cheng
    • , Mignon L. Loh
    • , Benjamin L. Ebert
    • , Soheil Meshinchi
    • , Torsten Haferlach
    •  & Charles G. Mullighan
  • Article |

    Cytogenetic and whole-genome-sequencing analyses using CEN-SELECT show that mitotic segregation errors generate a broad spectrum of chromosomal aberrations that recapitulate the complex structural features of cancer genomes.

    • Peter Ly
    • , Simon F. Brunner
    • , Ofer Shoshani
    • , Dong Hyun Kim
    • , Weijie Lan
    • , Tatyana Pyntikova
    • , Adrienne M. Flanagan
    • , Sam Behjati
    • , David C. Page
    • , Peter J. Campbell
    •  & Don W. Cleveland
  • Article |

    Transcriptional and epigenomic profiling of osteoblast and adipocyte differentiation shows that adipogenesis is driven by de novo activation of enhancers, whereas osteogenesis involves preestablished enhancers and depends on the activation of pro-osteogenic and antiadipogenic transcription factors.

    • Alexander Rauch
    • , Anders K. Haakonsson
    • , Jesper G. S. Madsen
    • , Mette Larsen
    • , Isabel Forss
    • , Martin R. Madsen
    • , Elvira L. Van Hauwaert
    • , Christian Wiwie
    • , Naja Z. Jespersen
    • , Michaela Tencerova
    • , Ronni Nielsen
    • , Bjørk D. Larsen
    • , Richard Röttger
    • , Jan Baumbach
    • , Camilla Scheele
    • , Moustapha Kassem
    •  & Susanne Mandrup
  • Article |

    Fate-mapping and clonal analysis show that bronchioalveolar stem cells (BASCs) become activated and respond distinctly to different lung injuries and differentiate into multiple cell types. Single-cell RNA-seq analysis identifies new BASC markers.

    • Qiaozhen Liu
    • , Kuo Liu
    • , Guizhong Cui
    • , Xiuzhen Huang
    • , Shun Yao
    • , Wenke Guo
    • , Zhen Qin
    • , Yan Li
    • , Rui Yang
    • , Wenjuan Pu
    • , Libo Zhang
    • , Lingjuan He
    • , Huan Zhao
    • , Wei Yu
    • , Muxue Tang
    • , Xueying Tian
    • , Dongqing Cai
    • , Yu Nie
    • , Shengshou Hu
    • , Tao Ren
    • , Zengyong Qiao
    • , Hefeng Huang
    • , Yi Arial Zeng
    • , Naihe Jing
    • , Guangdun Peng
    • , Hongbin Ji
    •  & Bin Zhou
  • Article | | Open Access

    High-quality de novo–assembled genomes of two cultivated allotetraploid cotton species and whole-genome comparative analyses provide insights into the evolution of cotton genomes and improvement of fiber quality and resilience to stress.

    • Yan Hu
    • , Jiedan Chen
    • , Lei Fang
    • , Zhiyuan Zhang
    • , Wei Ma
    • , Yongchao Niu
    • , Longzhen Ju
    • , Jieqiong Deng
    • , Ting Zhao
    • , Jinmin Lian
    • , Kobi Baruch
    • , David Fang
    • , Xia Liu
    • , Yong-ling Ruan
    • , Mehboob-ur Rahman
    • , Jinlei Han
    • , Kai Wang
    • , Qiong Wang
    • , Huaitong Wu
    • , Gaofu Mei
    • , Yihao Zang
    • , Zegang Han
    • , Chenyu Xu
    • , Weijuan Shen
    • , Duofeng Yang
    • , Zhanfeng Si
    • , Fan Dai
    • , Liangfeng Zou
    • , Fei Huang
    • , Yulin Bai
    • , Yugao Zhang
    • , Avital Brodt
    • , Hilla Ben-Hamo
    • , Xiefei Zhu
    • , Baoliang Zhou
    • , Xueying Guan
    • , Shuijin Zhu
    • , Xiaoya Chen
    •  & Tianzhen Zhang

Technical Reports

  • Technical Report |

    Linked-read analysis is a method for analyzing single-cell DNA-sequencing data that accurately identifies somatic single-nucleotide variants by using read-level phasing with nearby germline variants, enabling the characterization of mutational signatures and estimation of somatic mutation rates in single cells.

    • Craig L. Bohrson
    • , Alison R. Barton
    • , Michael A. Lodato
    • , Rachel E. Rodin
    • , Lovelace J. Luquette
    • , Vinay V. Viswanadham
    • , Doga C. Gulhan
    • , Isidro Cortés-Ciriano
    • , Maxwell A. Sherman
    • , Minseok Kwon
    • , Michael E. Coulter
    • , Alon Galor
    • , Christopher A. Walsh
    •  & Peter J. Park

Amendments & Corrections

  • Author Correction |

    • Miguel Verbitsky
    • , Rik Westland
    • , Alejandra Perez
    • , Krzysztof Kiryluk
    • , Qingxue Liu
    • , Priya Krithivasan
    • , Adele Mitrotti
    • , David A. Fasel
    • , Ekaterina Batourina
    • , Matthew G. Sampson
    • , Monica Bodria
    • , Max Werth
    • , Charlly Kao
    • , Jeremiah Martino
    • , Valentina P. Capone
    • , Asaf Vivante
    • , Shirlee Shril
    • , Byum Hee Kil
    • , Maddalena Marasa
    • , Jun Y. Zhang
    • , Young-Ji Na
    • , Tze Y. Lim
    • , Dina Ahram
    • , Patricia L. Weng
    • , Erin L. Heinzen
    • , Alba Carrea
    • , Giorgio Piaggio
    • , Loreto Gesualdo
    • , Valeria Manca
    • , Giuseppe Masnata
    • , Maddalena Gigante
    • , Daniele Cusi
    • , Claudia Izzi
    • , Francesco Scolari
    • , Joanna A. E. van Wijk
    • , Marijan Saraga
    • , Domenico Santoro
    • , Giovanni Conti
    • , Pasquale Zamboli
    • , Hope White
    • , Dorota Drozdz
    • , Katarzyna Zachwieja
    • , Monika Miklaszewska
    • , Marcin Tkaczyk
    • , Daria Tomczyk
    • , Anna Krakowska
    • , Przemyslaw Sikora
    • , Tomasz Jarmoliński
    • , Maria K. Borszewska-Kornacka
    • , Robert Pawluch
    • , Maria Szczepanska
    • , Piotr Adamczyk
    • , Malgorzata Mizerska-Wasiak
    • , Grazyna Krzemien
    • , Agnieszka Szmigielska
    • , Marcin Zaniew
    • , Mark G. Dobson
    • , John M. Darlow
    • , Prem Puri
    • , David E. Barton
    • , Susan L. Furth
    • , Bradley A. Warady
    • , Zoran Gucev
    • , Vladimir J. Lozanovski
    • , Velibor Tasic
    • , Isabella Pisani
    • , Landino Allegri
    • , Lida M. Rodas
    • , Josep M. Campistol
    • , Cécile Jeanpierre
    • , Shumyle Alam
    • , Pasquale Casale
    • , Craig S. Wong
    • , Fangming Lin
    • , Débora M. Miranda
    • , Eduardo A. Oliveira
    • , Ana Cristina Simoes-e-Silva
    • , Jonathan M. Barasch
    • , Brynn Levy
    • , Nan Wu
    • , Friedhelm Hildebrandt
    • , Gian Marco Ghiggeri
    • , Anna Latos-Bielenska
    • , Anna Materna-Kiryluk
    • , Feng Zhang
    • , Hakon Hakonarson
    • , Virginia E. Papaioannou
    • , Cathy L. Mendelsohn
    • , Ali G. Gharavi
    •  & Simone Sanna-Cherchi
  • Author Correction |

    • Patrick P. Edger
    • , Thomas J. Poorten
    • , Robert VanBuren
    • , Michael A. Hardigan
    • , Marivi Colle
    • , Michael R. McKain
    • , Ronald D. Smith
    • , Scott J. Teresi
    • , Andrew D. L. Nelson
    • , Ching Man Wai
    • , Elizabeth I. Alger
    • , Kevin A. Bird
    • , Alan E. Yocca
    • , Nathan Pumplin
    • , Shujun Ou
    • , Gil Ben-Zvi
    • , Avital Brodt
    • , Kobi Baruch
    • , Thomas Swale
    • , Lily Shiue
    • , Charlotte B. Acharya
    • , Glenn S. Cole
    • , Jeffrey P. Mower
    • , Kevin L. Childs
    • , Ning Jiang
    • , Eric Lyons
    • , Michael Freeling
    • , Joshua R. Puzey
    •  & Steven J. Knapp