Browse Articles

  • News & Views |

    Efforts to systematically characterize silencers in animal genomes have been limited. Two studies in this issue of Nature Genetics bring silencers into the spotlight, identifying these elements genome wide in human and mouse cells, and providing insights into their function.

    • Monica Della Rosa
    •  & Mikhail Spivakov
  • Article |

    Chromatin interaction analysis identifies PRC2-bound silencers in mESCs, which, when deleted in mice, can lead to developmental phenotypes. Silencers in pluripotent cells can transition into active tissue-specific enhancers during development.

    • Chew Yee Ngan
    • , Chee Hong Wong
    • , Harianto Tjong
    • , Wenbo Wang
    • , Rachel L. Goldfeder
    • , Cindy Choi
    • , Hao He
    • , Liang Gong
    • , Junyan Lin
    • , Barbara Urban
    • , Julianna Chow
    • , Meihong Li
    • , Joanne Lim
    • , Vivek Philip
    • , Stephen A. Murray
    • , Haoyi Wang
    •  & Chia-Lin Wei
  • Article |

    A genome-wide screen identifies silencer regions in human cells. Deletion of silencers linked to the transporter genes ABCC2 and ABCG2 causes their up-regulation and chemo-resistance.

    • Baoxu Pang
    •  & Michael P. Snyder
  • Letter |

    Deep mRNA sequencing at eight time points during memory CD4+ T cell activation identifies widespread dynamic allele-specific expression events that are enriched in HLA and other autoimmune disease loci.

    • Maria Gutierrez-Arcelus
    • , Yuriy Baglaenko
    • , Jatin Arora
    • , Susan Hannes
    • , Yang Luo
    • , Tiffany Amariuta
    • , Nikola Teslovich
    • , Deepak A. Rao
    • , Joerg Ermann
    • , A. Helena Jonsson
    • , Cristina Navarrete
    • , Stephen S. Rich
    • , Kent D. Taylor
    • , Jerome I. Rotter
    • , Peter K. Gregersen
    • , Tonu Esko
    • , Michael B. Brenner
    •  & Soumya Raychaudhuri
  • News & Views |

    Huntington’s disease is a severe progressive neurological disorder caused by a CAG-repeat expansion in the HTT gene. A small molecule shows therapeutic potential by inducing contraction of these expanded CAG repeats in cell and mouse models of the disease.

    • Michael D. Flower
    •  & Sarah J. Tabrizi
  • Article |

    Naphthyridine-azaquinolone specifically binds slipped-CAG DNA intermediates, induces contractions of expanded repeats and reduces mutant HTT protein aggregates in cell and animal models of Huntington’s disease.

    • Masayuki Nakamori
    • , Gagan B. Panigrahi
    • , Stella Lanni
    • , Terence Gall-Duncan
    • , Hideki Hayakawa
    • , Hana Tanaka
    • , Jennifer Luo
    • , Takahiro Otabe
    • , Jinxing Li
    • , Akihiro Sakata
    • , Marie-Christine Caron
    • , Niraj Joshi
    • , Tanya Prasolava
    • , Karen Chiang
    • , Jean-Yves Masson
    • , Marc S. Wold
    • , Xiaoxiao Wang
    • , Marietta Y. W. T. Lee
    • , John Huddleston
    • , Katherine M. Munson
    • , Scott Davidson
    • , Mehdi Layeghifard
    • , Lisa-Monique Edward
    • , Richard Gallon
    • , Mauro Santibanez-Koref
    • , Asako Murata
    • , Masanori P. Takahashi
    • , Evan E. Eichler
    • , Adam Shlien
    • , Kazuhiko Nakatani
    • , Hideki Mochizuki
    •  & Christopher E. Pearson
  • Author Correction |

    • Michelle Chan-Seng-Yue
    • , Jaeseung C. Kim
    • , Gavin W. Wilson
    • , Karen Ng
    • , Eugenia Flores Figueroa
    • , Grainne M. O’Kane
    • , Ashton A. Connor
    • , Robert E. Denroche
    • , Robert C. Grant
    • , Jessica McLeod
    • , Julie M. Wilson
    • , Gun Ho Jang
    • , Amy Zhang
    • , Sheng-Ben Liang
    • , Ayelet Borgida
    • , Dianne Chadwick
    • , Sangeetha Kalimuthu
    • , Ilinca Lungu
    • , John M. S. Bartlett
    • , Paul M. Krzyzanowski
    • , Vandana Sandhu
    • , Hervé Tiriac
    • , Fieke E. M. Froeling
    • , Joanna M. Karasinska
    • , James T. Topham
    • , Daniel J. Renouf
    • , David F. Schaeffer
    • , Steven J. M. Jones
    • , Marco A. Marra
    • , Janessa Laskin
    • , Runjan Chetty
    • , Lincoln D. Stein
    • , George Zogopoulos
    • , Benjamin Haibe-Kains
    • , Peter J. Campbell
    • , David A. Tuveson
    • , Jennifer J. Knox
    • , Sandra E. Fischer
    • , Steven Gallinger
    •  & Faiyaz Notta
  • Author Correction |

    • Pierre Vabres
    • , Arthur Sorlin
    • , Stanislav S. Kholmanskikh
    • , Bénédicte Demeer
    • , Judith St-Onge
    • , Yannis Duffourd
    • , Paul Kuentz
    • , Jean-Benoît Courcet
    • , Virginie Carmignac
    • , Philippine Garret
    • , Didier Bessis
    • , Odile Boute
    • , Alain Bron
    • , Guillaume Captier
    • , Esther Carmi
    • , Bernard Devauchelle
    • , David Geneviève
    • , Catherine Gondry-Jouet
    • , Laurent Guibaud
    • , Arnaud Lafon
    • , Michèle Mathieu-Dramard
    • , Julien Thevenon
    • , William B. Dobyns
    • , Geneviève Bernard
    • , Satyamaanasa Polubothu
    • , Francesca Faravelli
    • , Veronica A. Kinsler
    • , Christel Thauvin
    • , Laurence Faivre
    • , M. Elizabeth Ross
    •  & Jean-Baptiste Rivière
  • Author Correction |

    • Iris E. Jansen
    • , Jeanne E. Savage
    • , Kyoko Watanabe
    • , Julien Bryois
    • , Dylan M. Williams
    • , Stacy Steinberg
    • , Julia Sealock
    • , Ida K. Karlsson
    • , Sara Hägg
    • , Lavinia Athanasiu
    • , Nicola Voyle
    • , Petroula Proitsi
    • , Aree Witoelar
    • , Sven Stringer
    • , Dag Aarsland
    • , Ina S. Almdahl
    • , Fred Andersen
    • , Sverre Bergh
    • , Francesco Bettella
    • , Sigurbjorn Bjornsson
    • , Anne Brækhus
    • , Geir Bråthen
    • , Christiaan de Leeuw
    • , Rahul S. Desikan
    • , Srdjan Djurovic
    • , Logan Dumitrescu
    • , Tormod Fladby
    • , Timothy J. Hohman
    • , Palmi V. Jonsson
    • , Steven J. Kiddle
    • , Arvid Rongve
    • , Ingvild Saltvedt
    • , Sigrid B. Sando
    • , Geir Selbæk
    • , Maryam Shoai
    • , Nathan G. Skene
    • , Jon Snaedal
    • , Eystein Stordal
    • , Ingun D. Ulstein
    • , Yunpeng Wang
    • , Linda R. White
    • , John Hardy
    • , Jens Hjerling-Leffler
    • , Patrick F. Sullivan
    • , Wiesje M. van der Flier
    • , Richard Dobson
    • , Lea K. Davis
    • , Hreinn Stefansson
    • , Kari Stefansson
    • , Nancy L. Pedersen
    • , Stephan Ripke
    • , Ole A. Andreassen
    •  & Danielle Posthuma
  • Editorial |

    Given that it is based on heredity and has the ability to trace connections, genetics as a scientific discipline should be among those most attuned to diversity and global perspectives. Indigenous communities and scientists have much to contribute to genetics research, and they are making their voices heard. We celebrate these essential members of our larger genetics community, and we look forward to working together to learn from past examples, meet present challenges and support future opportunities.

  • Analysis
    | Open Access

    Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.

    • Isidro Cortés-Ciriano
    • , Jake June-Koo Lee
    • , Ruibin Xi
    • , Dhawal Jain
    • , Youngsook L. Jung
    • , Lixing Yang
    • , Dmitry Gordenin
    • , Leszek J. Klimczak
    • , Cheng-Zhong Zhang
    • , David S. Pellman
    • , Kadir C. Akdemir
    • , Eva G. Alvarez
    • , Adrian Baez-Ortega
    • , Rameen Beroukhim
    • , Paul C. Boutros
    • , David D. L. Bowtell
    • , Benedikt Brors
    • , Kathleen H. Burns
    • , Peter J. Campbell
    • , Kin Chan
    • , Ken Chen
    • , Isidro Cortés-Ciriano
    • , Ana Dueso-Barroso
    • , Andrew J. Dunford
    • , Paul A. Edwards
    • , Xavier Estivill
    • , Dariush Etemadmoghadam
    • , Lars Feuerbach
    • , J. Lynn Fink
    • , Milana Frenkel-Morgenstern
    • , Dale W. Garsed
    • , Mark Gerstein
    • , Dmitry A. Gordenin
    • , David Haan
    • , James E. Haber
    • , Julian M. Hess
    • , Barbara Hutter
    • , Marcin Imielinski
    • , David T. W. Jones
    • , Young Seok Ju
    • , Marat D. Kazanov
    • , Leszek J. Klimczak
    • , Youngil Koh
    • , Jan O. Korbel
    • , Kiran Kumar
    • , Eunjung Alice Lee
    • , Jake June-Koo Lee
    • , Yilong Li
    • , Andy G. Lynch
    • , Geoff Macintyre
    • , Florian Markowetz
    • , Iñigo Martincorena
    • , Alexander Martinez-Fundichely
    • , Satoru Miyano
    • , Hidewaki Nakagawa
    • , Fabio C. P. Navarro
    • , Stephan Ossowski
    • , Peter J. Park
    • , John V. Pearson
    • , Montserrat Puiggròs
    • , Karsten Rippe
    • , Nicola D. Roberts
    • , Steven A. Roberts
    • , Bernardo Rodriguez-Martin
    • , Steven E. Schumacher
    • , Ralph Scully
    • , Mark Shackleton
    • , Nikos Sidiropoulos
    • , Lina Sieverling
    • , Chip Stewart
    • , David Torrents
    • , Jose M. C. Tubio
    • , Izar Villasante
    • , Nicola Waddell
    • , Jeremiah A. Wala
    • , Joachim Weischenfeldt
    • , Lixing Yang
    • , Xiaotong Yao
    • , Sung-Soo Yoon
    • , Jorge Zamora
    • , Cheng-Zhong Zhang
    •  & Peter J. Park
  • Article |

    A mouse model that combines nitrosamide exposure with inducible, tissue-specific TP53 alterations is used to generate premalignant gastric organoids and provides insights into the development of gastric premalignancy.

    • Nilay S. Sethi
    • , Osamu Kikuchi
    • , Gina N. Duronio
    • , Matthew D. Stachler
    • , James M. McFarland
    • , Ruben Ferrer-Luna
    • , Yanxi Zhang
    • , Chunyang Bao
    • , Roderick Bronson
    • , Deepa Patil
    • , Francisco Sanchez-Vega
    • , Jie-Bin Liu
    • , Ewa Sicinska
    • , Jean-Bernard Lazaro
    • , Keith L. Ligon
    • , Rameen Beroukhim
    •  & Adam J. Bass
  • Article
    | Open Access

    Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

    • Marc Zapatka
    • , Ivan Borozan
    • , Daniel S. Brewer
    • , Murat Iskar
    • , Adam Grundhoff
    • , Malik Alawi
    • , Nikita Desai
    • , Holger Sültmann
    • , Holger Moch
    • , Malik Alawi
    • , Colin S. Cooper
    • , Roland Eils
    • , Vincent Ferretti
    • , Peter Lichter
    • , Ivan Borozan
    • , Daniel S. Brewer
    • , Colin S. Cooper
    • , Nikita Desai
    • , Roland Eils
    • , Vincent Ferretti
    • , Adam Grundhoff
    • , Murat Iskar
    • , Kortine Kleinheinz
    • , Peter Lichter
    • , Hidewaki Nakagawa
    • , Akinyemi I. Ojesina
    • , Chandra Sekhar Pedamallu
    • , Matthias Schlesner
    • , Xiaoping Su
    •  & Marc Zapatka
  • Analysis
    | Open Access

    Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

    • Yuan Yuan
    • , Young Seok Ju
    • , Youngwook Kim
    • , Jun Li
    • , Yumeng Wang
    • , Christopher J. Yoon
    • , Yang Yang
    • , Inigo Martincorena
    • , Chad J. Creighton
    • , John N. Weinstein
    • , Yanxun Xu
    • , Leng Han
    • , Hyung-Lae Kim
    • , Hidewaki Nakagawa
    • , Keunchil Park
    • , Peter J. Campbell
    •  & Han Liang
  • Article
    | Open Access

    A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

    • Kadir C. Akdemir
    • , Victoria T. Le
    • , Sahaana Chandran
    • , Yilong Li
    • , Roel G. Verhaak
    • , Rameen Beroukhim
    • , Peter J. Campbell
    • , Lynda Chin
    • , Jesse R. Dixon
    • , P. Andrew Futreal
    • , Kadir C. Akdemir
    • , Eva G. Alvarez
    • , Adrian Baez-Ortega
    • , Rameen Beroukhim
    • , Paul C. Boutros
    • , David D. L. Bowtell
    • , Benedikt Brors
    • , Kathleen H. Burns
    • , Peter J. Campbell
    • , Kin Chan
    • , Ken Chen
    • , Isidro Cortés-Ciriano
    • , Ana Dueso-Barroso
    • , Andrew J. Dunford
    • , Paul A. Edwards
    • , Xavier Estivill
    • , Dariush Etemadmoghadam
    • , Lars Feuerbach
    • , J. Lynn Fink
    • , Milana Frenkel-Morgenstern
    • , Dale W. Garsed
    • , Mark Gerstein
    • , Dmitry A. Gordenin
    • , David Haan
    • , James E. Haber
    • , Julian M. Hess
    • , Barbara Hutter
    • , Marcin Imielinski
    • , David T. W. Jones
    • , Young Seok Ju
    • , Marat D. Kazanov
    • , Leszek J. Klimczak
    • , Youngil Koh
    • , Jan O. Korbel
    • , Kiran Kumar
    • , Eunjung Alice Lee
    • , Jake June-Koo Lee
    • , Yilong Li
    • , Andy G. Lynch
    • , Geoff Macintyre
    • , Florian Markowetz
    • , Iñigo Martincorena
    • , Alexander Martinez-Fundichely
    • , Matthew Meyerson
    • , Satoru Miyano
    • , Hidewaki Nakagawa
    • , Fabio C. P. Navarro
    • , Stephan Ossowski
    • , Peter J. Park
    • , John V. Pearson
    • , Montserrat Puiggròs
    • , Karsten Rippe
    • , Nicola D. Roberts
    • , Steven A. Roberts
    • , Bernardo Rodriguez-Martin
    • , Steven E. Schumacher
    • , Ralph Scully
    • , Mark Shackleton
    • , Nikos Sidiropoulos
    • , Lina Sieverling
    • , Chip Stewart
    • , David Torrents
    • , Jose M. C. Tubio
    • , Izar Villasante
    • , Nicola Waddell
    • , Jeremiah A. Wala
    • , Joachim Weischenfeldt
    • , Lixing Yang
    • , Xiaotong Yao
    • , Sung-Soo Yoon
    • , Jorge Zamora
    •  & Cheng-Zhong Zhang
  • Article
    | Open Access

    An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

    • Bernardo Rodriguez-Martin
    • , Eva G. Alvarez
    • , Adrian Baez-Ortega
    • , Jorge Zamora
    • , Fran Supek
    • , Jonas Demeulemeester
    • , Martin Santamarina
    • , Young Seok Ju
    • , Javier Temes
    • , Daniel Garcia-Souto
    • , Harald Detering
    • , Yilong Li
    • , Jorge Rodriguez-Castro
    • , Ana Dueso-Barroso
    • , Alicia L. Bruzos
    • , Stefan C. Dentro
    • , Miguel G. Blanco
    • , Gianmarco Contino
    • , Daniel Ardeljan
    • , Marta Tojo
    • , Nicola D. Roberts
    • , Sonia Zumalave
    • , Paul A. W. Edwards
    • , Joachim Weischenfeldt
    • , Montserrat Puiggròs
    • , Zechen Chong
    • , Ken Chen
    • , Eunjung Alice Lee
    • , Jeremiah A. Wala
    • , Keiran Raine
    • , Adam Butler
    • , Sebastian M. Waszak
    • , Fabio C. P. Navarro
    • , Steven E. Schumacher
    • , Jean Monlong
    • , Francesco Maura
    • , Niccolo Bolli
    • , Guillaume Bourque
    • , Mark Gerstein
    • , Peter J. Park
    • , David C. Wedge
    • , Rameen Beroukhim
    • , David Torrents
    • , Jan O. Korbel
    • , Inigo Martincorena
    • , Rebecca C. Fitzgerald
    • , Peter Van Loo
    • , Haig H. Kazazian
    • , Kathleen H. Burns
    • , Kadir C. Akdemir
    • , Eva G. Alvarez
    • , Adrian Baez-Ortega
    • , Rameen Beroukhim
    • , Paul C. Boutros
    • , David D. L. Bowtell
    • , Benedikt Brors
    • , Kathleen H. Burns
    • , Peter J. Campbell
    • , Kin Chan
    • , Ken Chen
    • , Isidro Cortés-Ciriano
    • , Ana Dueso-Barroso
    • , Andrew J. Dunford
    • , Paul A. Edwards
    • , Xavier Estivill
    • , Dariush Etemadmoghadam
    • , Lars Feuerbach
    • , J. Lynn Fink
    • , Milana Frenkel-Morgenstern
    • , Dale W. Garsed
    • , Mark Gerstein
    • , Dmitry A. Gordenin
    • , David Haan
    • , James E. Haber
    • , Julian M. Hess
    • , Barbara Hutter
    • , Marcin Imielinski
    • , David T. W. Jones
    • , Young Seok Ju
    • , Marat D. Kazanov
    • , Leszek J. Klimczak
    • , Youngil Koh
    • , Jan O. Korbel
    • , Kiran Kumar
    • , Eunjung Alice Lee
    • , Jake June-Koo Lee
    • , Yilong Li
    • , Andy G. Lynch
    • , Geoff Macintyre
    • , Florian Markowetz
    • , Iñigo Martincorena
    • , Alexander Martinez-Fundichely
    • , Matthew Meyerson
    • , Satoru Miyano
    • , Hidewaki Nakagawa
    • , Fabio C. P. Navarro
    • , Stephan Ossowski
    • , Peter J. Park
    • , John V. Pearson
    • , Montserrat Puiggròs
    • , Karsten Rippe
    • , Nicola D. Roberts
    • , Steven A. Roberts
    • , Bernardo Rodriguez-Martin
    • , Steven E. Schumacher
    • , Ralph Scully
    • , Mark Shackleton
    • , Nikos Sidiropoulos
    • , Lina Sieverling
    • , Chip Stewart
    • , David Torrents
    • , Jose M. C. Tubio
    • , Izar Villasante
    • , Nicola Waddell
    • , Jeremiah A. Wala
    • , Joachim Weischenfeldt
    • , Lixing Yang
    • , Xiaotong Yao
    • , Sung-Soo Yoon
    • , Jorge Zamora
    • , Cheng-Zhong Zhang
    • , Peter J. Campbell
    •  & Jose M. C. Tubio
  • Article |

    MutPanning is a new method to detect cancer driver genes that identifies genes with an excess of mutations in unusual nucleotide contexts. Applying this to whole-exome sequencing data from 11,873 tumor–normal pairs identifies 460 driver genes.

    • Felix Dietlein
    • , Donate Weghorn
    • , Amaro Taylor-Weiner
    • , André Richters
    • , Brendan Reardon
    • , David Liu
    • , Eric S. Lander
    • , Eliezer M. Van Allen
    •  & Shamil R. Sunyaev
  • Article |

    Genomic and transcriptomic analysis of lung adenocarcinoma (LUAD) in Asia indicates that Asian LUADs have fewer mutations, lower driver prevalence and fewer copy number alterations than European LUADs.

    • Jianbin Chen
    • , Hechuan Yang
    • , Audrey Su Min Teo
    • , Lidyana Bte Amer
    • , Faranak Ghazi Sherbaf
    • , Chu Quan Tan
    • , Jacob Josiah Santiago Alvarez
    • , Bingxin Lu
    • , Jia Qi Lim
    • , Angela Takano
    • , Rahul Nahar
    • , Yin Yeng Lee
    • , Cheryl Zi Jin Phua
    • , Khi Pin Chua
    • , Lisda Suteja
    • , Pauline Jieqi Chen
    • , Mei Mei Chang
    • , Tina Puay Theng Koh
    • , Boon-Hean Ong
    • , Devanand Anantham
    • , Anne Ann Ling Hsu
    • , Apoorva Gogna
    • , Chow Wei Too
    • , Zaw Win Aung
    • , Yi Fei Lee
    • , Lanying Wang
    • , Tony Kiat Hon Lim
    • , Andreas Wilm
    • , Poh Sum Choi
    • , Poh Yong Ng
    • , Chee Keong Toh
    • , Wan-Teck Lim
    • , Siming Ma
    • , Bing Lim
    • , Jin Liu
    • , Wai Leong Tam
    • , Anders Jacobsen Skanderup
    • , Joe Poh Sheng Yeong
    • , Eng-Huat Tan
    • , Caretha L. Creasy
    • , Daniel Shao Weng Tan
    • , Axel M. Hillmer
    •  & Weiwei Zhai
  • Author Correction |

    • Sankari Nagarajan
    • , Shalini V. Rao
    • , Joseph Sutton
    • , Danya Cheeseman
    • , Shanade Dunn
    • , Evangelia K. Papachristou
    • , Jose-Enrique Gonzalez Prada
    • , Dominique-Laurent Couturier
    • , Sanjeev Kumar
    • , Kamal Kishore
    • , Chandra Sekhar Reddy Chilamakuri
    • , Silvia-Elena Glont
    • , Emily Archer Goode
    • , Cara Brodie
    • , Naomi Guppy
    • , Rachael Natrajan
    • , Alejandra Bruna
    • , Carlos Caldas
    • , Alasdair Russell
    • , Rasmus Siersbæk
    • , Kosuke Yusa
    • , Igor Chernukhin
    •  & Jason S. Carroll
  • Article |

    Multitrait genome-wide analysis of glaucoma and related phenotypes identifies new risk loci and enables development of a polygenic risk score to predict disease susceptibility and key clinical outcomes.

    • Jamie E. Craig
    • , Xikun Han
    • , Ayub Qassim
    • , Mark Hassall
    • , Jessica N. Cooke Bailey
    • , Tyler G. Kinzy
    • , Anthony P. Khawaja
    • , Jiyuan An
    • , Henry Marshall
    • , Puya Gharahkhani
    • , Robert P. Igo Jr.
    • , Stuart L. Graham
    • , Paul R. Healey
    • , Jue-Sheng Ong
    • , Tiger Zhou
    • , Owen Siggs
    • , Matthew H. Law
    • , Emmanuelle Souzeau
    • , Bronwyn Ridge
    • , Pirro G. Hysi
    • , Kathryn P. Burdon
    • , Richard A. Mills
    • , John Landers
    • , Jonathan B. Ruddle
    • , Ashish Agar
    • , Anna Galanopoulos
    • , Andrew J. R. White
    • , Colin E. Willoughby
    • , Nicholas H. Andrew
    • , Stephen Best
    • , Andrea L. Vincent
    • , Ivan Goldberg
    • , Graham Radford-Smith
    • , Nicholas G. Martin
    • , Grant W. Montgomery
    • , Veronique Vitart
    • , Rene Hoehn
    • , Robert Wojciechowski
    • , Jost B. Jonas
    • , Tin Aung
    • , Louis R. Pasquale
    • , Angela Jane Cree
    • , Sobha Sivaprasad
    • , Neeru A. Vallabh
    • , Ananth C. Viswanathan
    • , Francesca Pasutto
    • , Jonathan L. Haines
    • , Caroline C. W. Klaver
    • , Cornelia M. van Duijn
    • , Robert J. Casson
    • , Paul J. Foster
    • , Peng Tee Khaw
    • , Christopher J. Hammond
    • , David A. Mackey
    • , Paul Mitchell
    • , Andrew J. Lotery
    • , Janey L. Wiggs
    • , Alex W. Hewitt
    •  & Stuart MacGregor
  • Article |

    Genome-wide association analysis of 1,172 urinary metabolites identifies 240 metabolite–locus associations that when combined with UK Biobank data suggest novel metabolic mediators of disease and markers of disease risk.

    • Pascal Schlosser
    • , Yong Li
    • , Peggy Sekula
    • , Johannes Raffler
    • , Franziska Grundner-Culemann
    • , Maik Pietzner
    • , Yurong Cheng
    • , Matthias Wuttke
    • , Inga Steinbrenner
    • , Ulla T. Schultheiss
    • , Fruzsina Kotsis
    • , Tim Kacprowski
    • , Lukas Forer
    • , Birgit Hausknecht
    • , Arif B. Ekici
    • , Matthias Nauck
    • , Uwe Völker
    • , Gerd Walz
    • , Peter J. Oefner
    • , Florian Kronenberg
    • , Robert P. Mohney
    • , Michael Köttgen
    • , Karsten Suhre
    • , Kai-Uwe Eckardt
    • , Gabi Kastenmüller
    •  & Anna Köttgen
  • Letter |

    Experiments in developing human erythroid cells show that LIN28B controls hemoglobin switching by directly suppressing BCL11A translation, independently of its role in regulating let-7 microRNA biogenesis.

    • Anindita Basak
    • , Mathias Munschauer
    • , Caleb A. Lareau
    • , Kara E. Montbleau
    • , Jacob C. Ulirsch
    • , Christina R. Hartigan
    • , Monica Schenone
    • , John Lian
    • , Yaomei Wang
    • , Yumin Huang
    • , Xianfang Wu
    • , Lee Gehrke
    • , Charles M. Rice
    • , Xiuli An
    • , Helen A. Christou
    • , Narla Mohandas
    • , Steven A. Carr
    • , Jane-Jane Chen
    • , Stuart H. Orkin
    • , Eric S. Lander
    •  & Vijay G. Sankaran
  • Article |

    Whole-genome sequencing, transcriptome sequencing and single-cell analysis of primary and metastatic pancreatic adenocarcinoma identify molecular subtypes and intratumor heterogeneity.

    • Michelle Chan-Seng-Yue
    • , Jaeseung C. Kim
    • , Gavin W. Wilson
    • , Karen Ng
    • , Eugenia Flores Figueroa
    • , Grainne M. O’Kane
    • , Ashton A. Connor
    • , Robert E. Denroche
    • , Robert C. Grant
    • , Jessica McLeod
    • , Julie M. Wilson
    • , Gun Ho Jang
    • , Amy Zhang
    • , Anna Dodd
    • , Sheng-Ben Liang
    • , Ayelet Borgida
    • , Dianne Chadwick
    • , Sangeetha Kalimuthu
    • , Ilinca Lungu
    • , John M. S. Bartlett
    • , Paul M. Krzyzanowski
    • , Vandana Sandhu
    • , Hervé Tiriac
    • , Fieke E. M. Froeling
    • , Joanna M. Karasinska
    • , James T. Topham
    • , Daniel J. Renouf
    • , David F. Schaeffer
    • , Steven J. M. Jones
    • , Marco A. Marra
    • , Janessa Laskin
    • , Runjan Chetty
    • , Lincoln D. Stein
    • , George Zogopoulos
    • , Benjamin Haibe-Kains
    • , Peter J. Campbell
    • , David A. Tuveson
    • , Jennifer J. Knox
    • , Sandra E. Fischer
    • , Steven Gallinger
    •  & Faiyaz Notta
  • Article |

    A CRISPR–CAS9 screen, analysis of patient data, and functional in vivo and in vitro experiments identify a critical role for ARID1A in determining breast luminal cell identity and endocrine therapeutic response in estrogen-receptor-positive breast cancer.

    • Guotai Xu
    • , Sagar Chhangawala
    • , Emiliano Cocco
    • , Pedram Razavi
    • , Yanyan Cai
    • , Jordan E Otto
    • , Lorenzo Ferrando
    • , Pier Selenica
    • , Erik Ladewig
    • , Carmen Chan
    • , Arnaud Da Cruz Paula
    • , Matthew Witkin
    • , Yuanming Cheng
    • , Jane Park
    • , Cristian Serna-Tamayo
    • , HuiYong Zhao
    • , Fan Wu
    • , Mirna Sallaku
    • , Xuan Qu
    • , Alison Zhao
    • , Clayton K Collings
    • , Andrew R. D’Avino
    • , Komal Jhaveri
    • , Richard Koche
    • , Ross L. Levine
    • , Jorge S. Reis-Filho
    • , Cigall Kadoch
    • , Maurizio Scaltriti
    • , Christina S. Leslie
    • , José Baselga
    •  & Eneda Toska
  • Perspective |

    Recent advances in Hi-C, single-cell imaging and functional genetic studies warrant discussion on the functional relevance of topologically associating domains (TADs) and other classes of chromatin domains.

    • Jonathan A. Beagan
    •  & Jennifer E. Phillips-Cremins
  • Article |

    Fine-mapping of causal variants and integration of epigenetic and chromatin conformation data identify likely target genes for 150 breast cancer risk regions.

    • Laura Fachal
    • , Hugues Aschard
    • , Jonathan Beesley
    • , Daniel R. Barnes
    • , Jamie Allen
    • , Siddhartha Kar
    • , Karen A. Pooley
    • , Joe Dennis
    • , Kyriaki Michailidou
    • , Constance Turman
    • , Penny Soucy
    • , Audrey Lemaçon
    • , Michael Lush
    • , Jonathan P. Tyrer
    • , Maya Ghoussaini
    • , Mahdi Moradi Marjaneh
    • , Xia Jiang
    • , Simona Agata
    • , Kristiina Aittomäki
    • , M. Rosario Alonso
    • , Irene L. Andrulis
    • , Hoda Anton-Culver
    • , Natalia N. Antonenkova
    • , Adalgeir Arason
    • , Volker Arndt
    • , Kristan J. Aronson
    • , Banu K. Arun
    • , Bernd Auber
    • , Paul L. Auer
    • , Jacopo Azzollini
    • , Judith Balmaña
    • , Rosa B. Barkardottir
    • , Daniel Barrowdale
    • , Alicia Beeghly-Fadiel
    • , Javier Benitez
    • , Marina Bermisheva
    • , Katarzyna Białkowska
    • , Amie M. Blanco
    • , Carl Blomqvist
    • , William Blot
    • , Natalia V. Bogdanova
    • , Stig E. Bojesen
    • , Manjeet K. Bolla
    • , Bernardo Bonanni
    • , Ake Borg
    • , Kristin Bosse
    • , Hiltrud Brauch
    • , Hermann Brenner
    • , Ignacio Briceno
    • , Ian W. Brock
    • , Angela Brooks-Wilson
    • , Thomas Brüning
    • , Barbara Burwinkel
    • , Saundra S. Buys
    • , Qiuyin Cai
    • , Trinidad Caldés
    • , Maria A. Caligo
    • , Nicola J. Camp
    • , Ian Campbell
    • , Federico Canzian
    • , Jason S. Carroll
    • , Brian D. Carter
    • , Jose E. Castelao
    • , Jocelyne Chiquette
    • , Hans Christiansen
    • , Wendy K. Chung
    • , Kathleen B. M. Claes
    • , Christine L. Clarke
    • , Véronique Mari
    • , Pascaline Berthet
    • , Laurent Castera
    • , Dominique Vaur
    • , Hakima Lallaoui
    • , Yves-Jean Bignon
    • , Nancy Uhrhammer
    • , Valérie Bonadona
    • , Christine Lasset
    • , Françoise Révillion
    • , Paul Vennin
    • , Daniele Muller
    • , Denise Molina Gomes
    • , Olivier Ingster
    • , Isabelle Coupier
    • , Pascal Pujol
    • , Marie-Agnès Collonge-Rame
    • , Isabelle Mortemousque
    • , Odile Bera
    • , Mickaelle Rose
    • , Amandine Baurand
    • , Geoffrey Bertolone
    • , Laurence Faivre
    • , Hélène Dreyfus
    • , Dominique Leroux
    • , Laurence Venat-Bouvet
    • , Stéphane Bézieau
    • , Capucine Delnatte
    • , Jean Chiesa
    • , Brigitte Gilbert-Dussardier
    • , Paul Gesta
    • , Fabienne Prieur Prieur
    • , Myriam Bronner
    • , Johanna Sokolowska
    • , Florence Coulet
    • , Nadia Boutry-Kryza
    • , Alain Calender
    • , Sophie Giraud
    • , Mélanie Leone
    • , Sandra Fert-Ferrer
    • , Dominique Stoppa-Lyonnet
    • , Yue Jiao
    • , Fabienne Lesueur Lesueur
    • , Noura Mebirouk
    • , Emmanuelle Barouk-Simonet
    • , Virginie Bubien
    • , Michel Longy
    • , Nicolas Sevenet
    • , Laurence Gladieff
    • , Christine Toulas
    • , Audrey Reimineras
    • , Hagay Sobol
    • , Brigitte Bressac-de Paillerets
    • , Odile Cabaret
    • , Olivier Caron
    • , Marine Guillaud-Bataille
    • , Etienne Rouleau
    • , Muriel Belotti
    • , Bruno Buecher
    • , Sandrine Caputo
    • , Chrystelle Colas
    • , Antoine De Pauw
    • , Emmanuelle Fourme
    • , Marion Gauthier-Villars
    • , Lisa Golmard
    • , Virginie Moncoutier
    • , Claire Saule
    • , Alan Donaldson
    • , Alex Murray
    • , Angela Brady
    • , Carole Brewer
    • , Caroline Pottinger
    • , Clare Miller
    • , David Gallagher
    • , Helen Gregory
    • , Jackie Cook
    • , Jacqueline Eason
    • , Julian Adlard
    • , Julian Barwell
    • , Kai-Ren Ong
    • , Katie Snape
    • , Lisa Walker
    • , Louise Izatt
    • , Lucy Side
    • , Marc Tischkowitz
    • , Mark T. Rogers
    • , Mary E. Porteous
    • , Munaza Ahmed
    • , Patrick J. Morrison
    • , Paul Brennan
    • , Ros Eeles
    • , Rosemarie Davidson
    • , J. Margriet Collée
    • , Sten Cornelissen
    • , Fergus J. Couch
    • , Angela Cox
    • , Simon S. Cross
    • , Cezary Cybulski
    • , Kamila Czene
    • , Mary B. Daly
    • , Miguel de la Hoya
    • , Peter Devilee
    • , Orland Diez
    • , Yuan Chun Ding
    • , Gillian S. Dite
    • , Susan M. Domchek
    • , Thilo Dörk
    • , Isabel dos-Santos-Silva
    • , Arnaud Droit
    • , Stéphane Dubois
    • , Martine Dumont
    • , Mercedes Duran
    • , Lorraine Durcan
    • , Miriam Dwek
    • , Diana M. Eccles
    • , Christoph Engel
    • , Mikael Eriksson
    • , D. Gareth Evans
    • , Peter A. Fasching
    • , Olivia Fletcher
    • , Giuseppe Floris
    • , Henrik Flyger
    • , Lenka Foretova
    • , William D. Foulkes
    • , Eitan Friedman
    • , Lin Fritschi
    • , Debra Frost
    • , Marike Gabrielson
    • , Manuela Gago-Dominguez
    • , Gaetana Gambino
    • , Patricia A. Ganz
    • , Susan M. Gapstur
    • , Judy Garber
    • , José A. García-Sáenz
    • , Mia M. Gaudet
    • , Vassilios Georgoulias
    • , Graham G. Giles
    • , Gord Glendon
    • , Andrew K. Godwin
    • , Mark S. Goldberg
    • , David E. Goldgar
    • , Anna González-Neira
    • , Maria Grazia Tibiletti
    • , Mark H. Greene
    • , Mervi Grip
    • , Jacek Gronwald
    • , Anne Grundy
    • , Pascal Guénel
    • , Eric Hahnen
    • , Christopher A. Haiman
    • , Niclas Håkansson
    • , Per Hall
    • , Ute Hamann
    • , Patricia A. Harrington
    • , Jaana M. Hartikainen
    • , Mikael Hartman
    • , Wei He
    • , Catherine S. Healey
    • , Bernadette A. M. Heemskerk-Gerritsen
    • , Jane Heyworth
    • , Peter Hillemanns
    • , Frans B. L. Hogervorst
    • , Antoinette Hollestelle
    • , Maartje J. Hooning
    • , John L. Hopper
    • , Anthony Howell
    • , Guanmengqian Huang
    • , Peter J. Hulick
    • , Evgeny N. Imyanitov
    • , Adrienne Sexton
    • , Alice Christian
    • , Alison Trainer
    • , Allan Spigelman
    • , Andrew Fellows
    • , Andrew Shelling
    • , Anna De Fazio
    • , Anneke Blackburn
    • , Ashley Crook
    • , Bettina Meiser
    • , Briony Patterson
    • , Christine Clarke
    • , Christobel Saunders
    • , Clare Hunt
    • , Clare Scott
    • , David Amor
    • , Deb Marsh
    • , Edward Edkins
    • , Elizabeth Salisbury
    • , Eric Haan
    • , Eveline Neidermayr
    • , Finlay Macrea
    • , Gelareh Farshid
    • , Geoff Lindeman
    • , Georgia Trench
    • , Graham Mann
    • , Graham Giles
    • , Grantley Gill
    • , Heather Thorne
    • , Ian Campbell
    • , Ian Hickie
    • , Ingrid Winship
    • , James Flanagan
    • , James Kollias
    • , Jane Visvader
    • , Jennifer Stone
    • , Jessica Taylor
    • , Jo Burke
    • , Jodi Saunus
    • , John Forbes
    • , John Hopper
    • , Jonathan Beesley
    • , Judy Kirk
    • , Juliet French
    • , Kathy Tucker
    • , Kathy Wu
    • , Kelly Phillips
    • , Lara Lipton
    • , Leslie Andrews
    • , Lizz Lobb
    • , Logan Walker
    • , Maira Kentwell
    • , Mandy Spurdle
    • , Margaret Cummings
    • , Margaret Gleeson
    • , Marion Harris
    • , Mark Jenkins
    • , Mary Anne Young
    • , Martin Delatycki
    • , Mathew Wallis
    • , Matthew Burgess
    • , Melanie Price
    • , Melissa Brown
    • , Melissa Southey
    • , Michael Bogwitz
    • , Michael Field
    • , Michael Friedlander
    • , Michael Gattas
    • , Mona Saleh
    • , Nick Hayward
    • , Nick Pachter
    • , Paul Cohen
    • , Pascal Duijf
    • , Paul James
    • , Pete Simpson
    • , Peter Fong
    • , Phyllis Butow
    • , Rachael Williams
    • , Rick Kefford
    • , Rodney Scott
    • , Roger Milne
    • , Rosemary Balleine
    • , Sarah–Jane Dawson
    • , Sheau Lok
    • , Shona O’Connell
    • , Sian Greening
    • , Sophie Nightingale
    • , Stacey Edwards
    • , Stephen Fox
    • , Sue-Anne McLachlan
    • , Sunil Lakhani
    • , Yoland Antill
    • , Cora Aalfs
    • , Hanne Meijers-Heijboer
    • , Klaartje van Engelen
    • , Hans Gille
    • , Ingrid Boere
    • , Margriet Collée
    • , Carolien van Deurzen
    • , Maartje Hooning
    • , Inge-Marie Obdeijn
    • , Ans van den Ouweland
    • , Caroline Seynaeve
    • , Sabine Siesling
    • , Janneke Verloop
    • , Christi van Asperen
    • , Peter Devilee
    • , Twiggy van Cronenburg
    • , Rien Blok
    • , Maaike de Boer
    • , Encarna Gómez Garcia
    • , Muriel Adank
    • , Frans Hogervorst
    • , Denise Jenner
    • , Flora van Leeuwen
    • , Matti Rookus
    • , Nicola Russell
    • , Marjanka Schmidt
    • , Sandra van den Belt-Dusebout
    • , Carolien Kets
    • , Arjen Mensenkamp
    • , Truuske de Bock
    • , Annemieke van der Hout
    • , Marian Mourits
    • , Jan Oosterwijk
    • , Margreet Ausems
    • , Marco Koudijs
    • , Christine Clarke
    • , Deborah Marsh
    • , Rodney Scott
    • , Robert Baxter
    • , Desmond Yip
    • , Jane Carpenter
    • , Alison Davis
    • , Nirmala Pathmanathan
    • , Peter Simpson
    • , Dinny Graham
    • , Mythily Sachchithananthan
    • , Claudine Isaacs
    • , Motoki Iwasaki
    • , Agnes Jager
    • , Milena Jakimovska
    • , Anna Jakubowska
    • , Paul A. James
    • , Ramunas Janavicius
    • , Rachel C. Jankowitz
    • , Esther M. John
    • , Nichola Johnson
    • , Michael E. Jones
    • , Arja Jukkola-Vuorinen
    • , Audrey Jung
    • , Rudolf Kaaks
    • , Daehee Kang
    • , Pooja Middha Kapoor
    • , Beth Y. Karlan
    • , Renske Keeman
    • , Michael J. Kerin
    • , Elza Khusnutdinova
    • , Johanna I. Kiiski
    • , Judy Kirk
    • , Cari M. Kitahara
    • , Yon-Dschun Ko
    • , Irene Konstantopoulou
    • , Veli-Matti Kosma
    • , Stella Koutros
    • , Katerina Kubelka-Sabit
    • , Ava Kwong
    • , Kyriacos Kyriacou
    • , Yael Laitman
    • , Diether Lambrechts
    • , Eunjung Lee
    • , Goska Leslie
    • , Jenny Lester
    • , Fabienne Lesueur
    • , Annika Lindblom
    • , Wing-Yee Lo
    • , Jirong Long
    • , Artitaya Lophatananon
    • , Jennifer T. Loud
    • , Jan Lubiński
    • , Robert J. MacInnis
    • , Tom Maishman
    • , Enes Makalic
    • , Arto Mannermaa
    • , Mehdi Manoochehri
    • , Siranoush Manoukian
    • , Sara Margolin
    • , Maria Elena Martinez
    • , Keitaro Matsuo
    • , Tabea Maurer
    • , Dimitrios Mavroudis
    • , Rebecca Mayes
    • , Lesley McGuffog
    • , Catriona McLean
    • , Noura Mebirouk
    • , Alfons Meindl
    • , Austin Miller
    • , Nicola Miller
    • , Marco Montagna
    • , Fernando Moreno
    • , Kenneth Muir
    • , Anna Marie Mulligan
    • , Victor M. Muñoz-Garzon
    • , Taru A. Muranen
    • , Steven A. Narod
    • , Rami Nassir
    • , Katherine L. Nathanson
    • , Susan L. Neuhausen
    • , Heli Nevanlinna
    • , Patrick Neven
    • , Finn C. Nielsen
    • , Liene Nikitina-Zake
    • , Aaron Norman
    • , Kenneth Offit
    • , Edith Olah
    • , Olufunmilayo I. Olopade
    • , Håkan Olsson
    • , Nick Orr
    • , Ana Osorio
    • , V. Shane Pankratz
    • , Janos Papp
    • , Sue K. Park
    • , Tjoung-Won Park-Simon
    • , Michael T. Parsons
    • , James Paul
    • , Inge Sokilde Pedersen
    • , Bernard Peissel
    • , Beth Peshkin
    • , Paolo Peterlongo
    • , Julian Peto
    • , Dijana Plaseska-Karanfilska
    • , Karolina Prajzendanc
    • , Ross Prentice
    • , Nadege Presneau
    • , Darya Prokofyeva
    • , Miquel Angel Pujana
    • , Katri Pylkäs
    • , Paolo Radice
    • , Susan J. Ramus
    • , Johanna Rantala
    • , Rohini Rau-Murthy
    • , Gad Rennert
    • , Harvey A. Risch
    • , Mark Robson
    • , Atocha Romero
    • , Maria Rossing
    • , Emmanouil Saloustros
    • , Estela Sánchez-Herrero
    • , Dale P. Sandler
    • , Marta Santamariña
    • , Christobel Saunders
    • , Elinor J. Sawyer
    • , Maren T. Scheuner
    • , Daniel F. Schmidt
    • , Rita K. Schmutzler
    • , Andreas Schneeweiss
    • , Minouk J. Schoemaker
    • , Ben Schöttker
    • , Peter Schürmann
    • , Christopher Scott
    • , Rodney J. Scott
    • , Leigha Senter
    • , Caroline M. Seynaeve
    • , Mitul Shah
    • , Priyanka Sharma
    • , Chen-Yang Shen
    • , Xiao-Ou Shu
    • , Christian F. Singer
    • , Thomas P. Slavin
    • , Snezhana Smichkoska
    • , Melissa C. Southey
    • , John J. Spinelli
    • , Amanda B. Spurdle
    • , Jennifer Stone
    • , Dominique Stoppa-Lyonnet
    • , Christian Sutter
    • , Anthony J. Swerdlow
    • , Rulla M. Tamimi
    • , Yen Yen Tan
    • , William J. Tapper
    • , Jack A. Taylor
    • , Manuel R. Teixeira
    • , Maria Tengström
    • , Soo Hwang Teo
    • , Mary Beth Terry
    • , Alex Teulé
    • , Mads Thomassen
    • , Darcy L. Thull
    • , Marc Tischkowitz
    • , Amanda E. Toland
    • , Rob A. E. M. Tollenaar
    • , Ian Tomlinson
    • , Diana Torres
    • , Gabriela Torres-Mejía
    • , Melissa A. Troester
    • , Thérèse Truong
    • , Nadine Tung
    • , Maria Tzardi
    • , Hans-Ulrich Ulmer
    • , Celine M. Vachon
    • , Christi J. van Asperen
    • , Lizet E. van der Kolk
    • , Elizabeth J. van Rensburg
    • , Ana Vega
    • , Alessandra Viel
    • , Joseph Vijai
    • , Maartje J. Vogel
    • , Qin Wang
    • , Barbara Wappenschmidt
    • , Clarice R. Weinberg
    • , Jeffrey N. Weitzel
    • , Camilla Wendt
    • , Hans Wildiers
    • , Robert Winqvist
    • , Alicja Wolk
    • , Anna H. Wu
    • , Drakoulis Yannoukakos
    • , Yan Zhang
    • , Wei Zheng
    • , David Hunter
    • , Paul D. P. Pharoah
    • , Jenny Chang-Claude
    • , Montserrat García-Closas
    • , Marjanka K. Schmidt
    • , Roger L. Milne
    • , Vessela N. Kristensen
    • , Juliet D. French
    • , Stacey L. Edwards
    • , Antonis C. Antoniou
    • , Georgia Chenevix-Trench
    • , Jacques Simard
    • , Douglas F. Easton
    • , Peter Kraft
    •  & Alison M. Dunning
  • Editorial |

    As we usher in a new year of a new decade and ponder what the future will bring for the genetics field, we wish to reflect on some specific areas related to diversity, privacy and genome editing that require attention and vigilance from the community.

  • Article |

    pgFARM (paired guide RNAs for alternative exon removal) is a CRISPR–Cas9-based approach to manipulate alternative splicing and identify functional roles for individual exons, including poison exons with essential and tumor-suppressor roles.

    • James D. Thomas
    • , Jacob T. Polaski
    • , Qing Feng
    • , Emma J. De Neef
    • , Emma R. Hoppe
    • , Maria V. McSharry
    • , Joseph Pangallo
    • , Austin M. Gabel
    • , Andrea E. Belleville
    • , Jacqueline Watson
    • , Naomi T. Nkinsi
    • , Alice H. Berger
    •  & Robert K. Bradley
  • Article |

    Whole-genome sequencing and phylogenetic analysis of nearly 400 esophageal adenocarcinoma samples suggest a model of rapid subclone spreading from the primary tumor to multiple metastatic sites, which the authors term ‘clonal diaspora’.

    • Ayesha Noorani
    • , Xiaodun Li
    • , Martin Goddard
    • , Jason Crawte
    • , Ludmil B. Alexandrov
    • , Maria Secrier
    • , Matthew D. Eldridge
    • , Lawrence Bower
    • , Jamie Weaver
    • , Pierre Lao-Sirieix
    • , Inigo Martincorena
    • , Irene Debiram-Beecham
    • , Nicola Grehan
    • , Shona MacRae
    • , Shalini Malhotra
    • , Ahmad Miremadi
    • , Tabitha Thomas
    • , Sarah Galbraith
    • , Lorraine Petersen
    • , Stephen D. Preston
    • , David Gilligan
    • , Andrew Hindmarsh
    • , Richard H. Hardwick
    • , Michael R. Stratton
    • , David C. Wedge
    •  & Rebecca C. Fitzgerald
  • Article
    | Open Access

    Analysis of a near-chromosomal genome assembly and transcriptome profiling of the Indian cobra identifies genes expressed in the venom glands. These data should help develop a new antivenom.

    • Kushal Suryamohan
    • , Sajesh P. Krishnankutty
    • , Joseph Guillory
    • , Matthew Jevit
    • , Markus S. Schröder
    • , Meng Wu
    • , Boney Kuriakose
    • , Oommen K. Mathew
    • , Rajadurai C. Perumal
    • , Ivan Koludarov
    • , Leonard D. Goldstein
    • , Kate Senger
    • , Mandumpala Davis Dixon
    • , Dinesh Velayutham
    • , Derek Vargas
    • , Subhra Chaudhuri
    • , Megha Muraleedharan
    • , Ridhi Goel
    • , Ying-Jiun J. Chen
    • , Aakrosh Ratan
    • , Peter Liu
    • , Brendan Faherty
    • , Guillermo de la Rosa
    • , Hiroki Shibata
    • , Miriam Baca
    • , Meredith Sagolla
    • , James Ziai
    • , Gus A. Wright
    • , Domagoj Vucic
    • , Sangeetha Mohan
    • , Aju Antony
    • , Jeremy Stinson
    • , Donald S. Kirkpatrick
    • , Rami N. Hannoush
    • , Steffen Durinck
    • , Zora Modrusan
    • , Eric W. Stawiski
    • , Kristen Wiley
    • , Terje Raudsepp
    • , R. Manjunatha Kini
    • , Arun Zachariah
    •  & Somasekar Seshagiri
  • Article |

    ARID1A and other SWI/SNF components are critical for response to estrogen-receptor antagonists in breast cancer. SWI/SNF-specific gene knockouts lead to drug resistance and ARID1A mutations are more frequent in resistant tumors from patients.

    • Sankari Nagarajan
    • , Shalini V. Rao
    • , Joseph Sutton
    • , Danya Cheeseman
    • , Shanade Dunn
    • , Evangelia K. Papachristou
    • , Jose-Enrique Gonzalez Prada
    • , Dominique-Laurent Couturier
    • , Sanjeev Kumar
    • , Kamal Kishore
    • , Chandra Sekhar Reddy Chilamakuri
    • , Silvia-Elena Glont
    • , Emily Archer Goode
    • , Cara Brodie
    • , Naomi Guppy
    • , Rachael Natrajan
    • , Alejandra Bruna
    • , Carlos Caldas
    • , Alasdair Russell
    • , Rasmus Siersbæk
    • , Kosuke Yusa
    • , Igor Chernukhin
    •  & Jason S. Carroll
  • News & Views |

    RNA:DNA hybrids that form across genomes control a wide range of biological processes. A new study shows that N6-methyladenosine (m6A) modification on the RNA moieties regulates the formation and genome integrity of these hybrids. This finding opens a new avenue of research on how RNA modifications (the ‘epitranscriptome’) can help control genome maintenance.

    • Aline Marnef
    •  & Gaëlle Legube
  • Comment |

    The 11th International Conference on Rare Diseases and Orphan Drugs (ICORD), South Africa, included the Africa-Rare initiative launch and facilitated multi-stakeholder engagement in the challenges facing, and opportunities for, Africans living with rare diseases. The following ICORD Global Call to Action, developed in collaboration with the International Rare Diseases Research Consortium, synthesizes the outcomes of the deliberations and emphasizes the international collaborative efforts required to address the global effects of rare diseases on public health.

    • Gareth S. Baynam
    • , Stephen Groft
    • , Francois H. van der Westhuizen
    • , Safiyya D. Gassman
    • , Kelly du Plessis
    • , Emily P. Coles
    • , Eda Selebatso
    • , Moses Selebatso
    • , Boikobo Gaobinelwe
    • , Tebogo Selebatso
    • , Dipesalema Joel
    • , Virginia A. Llera
    • , Barend C. Vorster
    • , Barbara Wuebbels
    • , Benjamin Djoudalbaye
    • , Christopher P. Austin
    • , Judit Kumuthini
    • , John Forman
    • , Petra Kaufmann
    • , James Chipeta
    • , Désirée Gavhed
    • , Annika Larsson
    • , Maja Stojiljkovic
    • , Ann Nordgren
    • , Emilio J. A. Roldan
    • , Domenica Taruscio
    • , Durhane Wong-Rieger
    • , Kristen Nowak
    • , Gemma A. Bilkey
    • , Simon Easteal
    • , Sarah Bowdin
    • , Juergen K. V. Reichardt
    • , Sergi Beltran
    • , Kenjiro Kosaki
    • , Clara D. M. van Karnebeek
    • , Mengchun Gong
    • , Zhang Shuyang
    • , Ruty Mehrian-Shai
    • , David R. Adams
    • , Ratna D. Puri
    • , Feng Zhang
    • , Nicholas Pachter
    • , Maximilian Muenke
    • , Christoffer Nellaker
    • , William A. Gahl
    • , Helene Cederroth
    • , Stephanie Broley
    • , Maryke Schoonen
    • , Kym M. Boycott
    •  & Manuel Posada
  • Article |

    Resequencing and genome-wide association analysis of 683 common bean accessions across different latitudes identifies 505 loci associated with yield components, of which seed size, flowering and harvest maturity traits are stable across environments.

    • Jing Wu
    • , Lanfen Wang
    • , Junjie Fu
    • , Jibao Chen
    • , Shuhong Wei
    • , Shilong Zhang
    • , Jie Zhang
    • , Yongsheng Tang
    • , Mingli Chen
    • , Jifeng Zhu
    • , Lei Lei
    • , Qinghe Geng
    • , Chunliang Liu
    • , Lei Wu
    • , Xiaoming Li
    • , Xiaoli Wang
    • , Qiang Wang
    • , Zhaoli Wang
    • , Shilai Xing
    • , Haikuan Zhang
    • , Matthew W. Blair
    •  & Shumin Wang
  • Letter |

    N6-methyladenosine (m6A) is prevalent at RNA:DNA hybrids in human pluripotent stem cells. The m6A reader YTHDF2 interacts with R-loop-enriched loci in dividing cells, and YTHDF2 loss leads to increased R-loop levels and accumulation of γH2AX.

    • Abdulkadir Abakir
    • , Tom C. Giles
    • , Agnese Cristini
    • , Jeremy M. Foster
    • , Nan Dai
    • , Marta Starczak
    • , Alejandro Rubio-Roldan
    • , Miaomiao Li
    • , Maria Eleftheriou
    • , James Crutchley
    • , Luke Flatt
    • , Lorraine Young
    • , Daniel J. Gaffney
    • , Chris Denning
    • , Bjørn Dalhus
    • , Richard D. Emes
    • , Daniel Gackowski
    • , Ivan R. Corrêa Jr
    • , Jose L. Garcia-Perez
    • , Arne Klungland
    • , Natalia Gromak
    •  & Alexey Ruzov
  • Letter |

    Combined genomic and transcriptomic approaches identify the landscape of extrachromosomal circular DNA in neuroblastoma and reveal that extrachromosomal circular DNA is a major source of somatic rearrangements.

    • Richard P. Koche
    • , Elias Rodriguez-Fos
    • , Konstantin Helmsauer
    • , Martin Burkert
    • , Ian C. MacArthur
    • , Jesper Maag
    • , Rocio Chamorro
    • , Natalia Munoz-Perez
    • , Montserrat Puiggròs
    • , Heathcliff Dorado Garcia
    • , Yi Bei
    • , Claudia Röefzaad
    • , Victor Bardinet
    • , Annabell Szymansky
    • , Annika Winkler
    • , Theresa Thole
    • , Natalie Timme
    • , Katharina Kasack
    • , Steffen Fuchs
    • , Filippos Klironomos
    • , Nina Thiessen
    • , Eric Blanc
    • , Karin Schmelz
    • , Annette Künkele
    • , Patrick Hundsdörfer
    • , Carolina Rosswog
    • , Jessica Theissen
    • , Dieter Beule
    • , Hedwig Deubzer
    • , Sascha Sauer
    • , Joern Toedling
    • , Matthias Fischer
    • , Falk Hertwig
    • , Roland F. Schwarz
    • , Angelika Eggert
    • , David Torrents
    • , Johannes H. Schulte
    •  & Anton G. Henssen
  • Article |

    Genome-wide maps of chromatin dynamics during mouse gastrulation highlight a unique bivalent signature at developmental genes in E6.5 epiblast cells. KMT2B is essential for bivalent H3K4me3 at E6.5.

    • Yunlong Xiang
    • , Yu Zhang
    • , Qianhua Xu
    • , Chen Zhou
    • , Bofeng Liu
    • , Zhenhai Du
    • , Ke Zhang
    • , Bingjie Zhang
    • , Xiaoxiao Wang
    • , Srimonta Gayen
    • , Ling Liu
    • , Yao Wang
    • , Yuanyuan Li
    • , Qiujun Wang
    • , Sundeep Kalantry
    • , Lei Li
    •  & Wei Xie
  • Letter |

    Mutations in ADAMTS19 lead to progressive heart valve disease in humans. Analysis of mice lacking Adamts19 highlights the role of a Wnt–Adamts19–Klf2 axis in proper valve function.

    • Florian Wünnemann
    • , Asaf Ta-Shma
    • , Christoph Preuss
    • , Severine Leclerc
    • , Patrick Piet van Vliet
    • , Andrea Oneglia
    • , Maryse Thibeault
    • , Emily Nordquist
    • , Joy Lincoln
    • , Franka Scharfenberg
    • , Christoph Becker-Pauly
    • , Philipp Hofmann
    • , Kirstin Hoff
    • , Enrique Audain
    • , Hans-Heiner Kramer
    • , Wojciech Makalowski
    • , Amiram Nir
    • , Sebastian S. Gerety
    • , Matthew Hurles
    • , Johanna Comes
    • , Anne Fournier
    • , Hanna Osinska
    • , Jeffrey Robins
    • , Michel Pucéat
    • , Harry C. Dietz
    • , Andrew S. McCallion
    • , Gregor Andelfinger
    • , Bart L. Loeys
    • , Lut Van Laer
    • , Per Eriksson
    • , Salah A. Mohamed
    • , Luc Mertens
    • , Anders Franco-Cereceda
    • , Seema Mital
    • , Orly Elpeleg
    • , Marc-Phillip Hitz
    •  & Gregor Andelfinger
  • Article |

    Oncogenic MYC expression involves super-enhancer-mediated tethering of MYC alleles to nuclear pores, thus increasing messenger RNA export. This is regulated by AHCTF1 and β-catenin.

    • Barbara A. Scholz
    • , Noriyuki Sumida
    • , Carolina Diettrich Mallet de Lima
    • , Ilyas Chachoua
    • , Mirco Martino
    • , Ilias Tzelepis
    • , Andrej Nikoshkov
    • , Honglei Zhao
    • , Rashid Mehmood
    • , Emmanouil G. Sifakis
    • , Deeksha Bhartiya
    • , Anita Göndör
    •  & Rolf Ohlsson
  • Letter |

    Combining CRISPRi-FlowFISH to perturb enhancers with an activity-by-contact model to predict complex connections allows systematic mapping of enhancer–gene connections in a given cell type, on the basis of chromatin-state measurements.

    • Charles P. Fulco
    • , Joseph Nasser
    • , Thouis R. Jones
    • , Glen Munson
    • , Drew T. Bergman
    • , Vidya Subramanian
    • , Sharon R. Grossman
    • , Rockwell Anyoha
    • , Benjamin R. Doughty
    • , Tejal A. Patwardhan
    • , Tung H. Nguyen
    • , Michael Kane
    • , Elizabeth M. Perez
    • , Neva C. Durand
    • , Caleb A. Lareau
    • , Elena K. Stamenova
    • , Erez Lieberman Aiden
    • , Eric S. Lander
    •  & Jesse M. Engreitz
  • News & Views |

    A new study presents a powerful experimental approach, CRISPRi-FlowFISH, for mapping regulatory interactions, and uses it to characterize thousands of putative enhancer–gene pairs. The results suggest that most current approaches for predicting enhancer–gene interactions perform poorly, but a simple mathematical model combining distance with enhancer activity shows promise.

    • Daniel J. Gaffney
  • Article |

    High levels of histone acetylation at rhabdomyosarcoma SEs, including SOX8, are detrimental to transcription via exclusion of RNA Pol II, but not BRD4, from phase condensates.

    • Berkley E. Gryder
    • , Silvia Pomella
    • , Carly Sayers
    • , Xiaoli S. Wu
    • , Young Song
    • , Anna M. Chiarella
    • , Sukriti Bagchi
    • , Hsien-Chao Chou
    • , Ranu S. Sinniah
    • , Ashley Walton
    • , Xinyu Wen
    • , Rossella Rota
    • , Nathaniel A. Hathaway
    • , Keji Zhao
    • , Jiji Chen
    • , Christopher R. Vakoc
    • , Jack F. Shern
    • , Benjamin Z. Stanton
    •  & Javed Khan
  • Editorial |

    As the year comes to a close and we start to look ahead to 2020, we thought that we would highlight some of our favorite Nature Genetics papers from 2019. This snapshot also captures some of the topics and themes in genetics that we are most excited to see develop in the near future.