Cancer genomics

Cancer genomics is the study of the totality of DNA sequence and gene expression differences between tumour cells and normal host cells. It aims to understand the genetic basis of tumour cell proliferation and the evolution of the cancer genome under mutation and selection by the body environment, the immune system and therapeutic interventions.

Latest Research and Reviews

  • Research
    | Open Access

    Immunoglobulin (Ig) rearrangement and translocation information are usually obtained by targeted sequencing of the respective loci. Here, the authors present the IgCaller algorithm, which extracts Ig heavy and light chain genetic properties from short-read whole-genome sequencing results to provide a feasible alternative to direct sequencing.

    • Ferran Nadeu
    • , Rut Mas-de-les-Valls
    • , Alba Navarro
    • , Romina Royo
    • , Silvia Martín
    • , Neus Villamor
    • , Helena Suárez-Cisneros
    • , Rosó Mares
    • , Junyan Lu
    • , Anna Enjuanes
    • , Alfredo Rivas-Delgado
    • , Marta Aymerich
    • , Tycho Baumann
    • , Dolors Colomer
    • , Julio Delgado
    • , Ryan D. Morin
    • , Thorsten Zenz
    • , Xose S. Puente
    • , Peter J. Campbell
    • , Sílvia Beà
    • , Francesco Maura
    •  & Elías Campo
  • Research
    | Open Access

    • Masahiro Sekiguchi
    • , Masafumi Seki
    • , Tomoko Kawai
    • , Kenichi Yoshida
    • , Misa Yoshida
    • , Tomoya Isobe
    • , Noriko Hoshino
    • , Ryota Shirai
    • , Mio Tanaka
    • , Ryota Souzaki
    • , Kentaro Watanabe
    • , Yuki Arakawa
    • , Yasuhito Nannya
    • , Hiromichi Suzuki
    • , Yoichi Fujii
    • , Keisuke Kataoka
    • , Yuichi Shiraishi
    • , Kenichi Chiba
    • , Hiroko Tanaka
    • , Teppei Shimamura
    • , Yusuke Sato
    • , Aiko Sato-Otsubo
    • , Shunsuke Kimura
    • , Yasuo Kubota
    • , Mitsuteru Hiwatari
    • , Katsuyoshi Koh
    • , Yasuhide Hayashi
    • , Yutaka Kanamori
    • , Mureo Kasahara
    • , Kenichi Kohashi
    • , Motohiro Kato
    • , Takako Yoshioka
    • , Kimikazu Matsumoto
    • , Akira Oka
    • , Tomoaki Taguchi
    • , Masashi Sanada
    • , Yukichi Tanaka
    • , Satoru Miyano
    • , Kenichiro Hata
    • , Seishi Ogawa
    •  & Junko Takita
  • Research
    | Open Access

    The Pan-Cancer Analysis of Whole Genomes project generated a vast array of data. In this article, the authors describe five different online resources to enable readers to explore and visualize the data.

    • Mary J. Goldman
    • , Junjun Zhang
    • , Nuno A. Fonseca
    • , Isidro Cortés-Ciriano
    • , Qian Xiang
    • , Brian Craft
    • , Elena Piñeiro-Yáñez
    • , Brian D. O’Connor
    • , Wojciech Bazant
    • , Elisabet Barrera
    • , Alfonso Muñoz-Pomer
    • , Robert Petryszak
    • , Anja Füllgrabe
    • , Fatima Al-Shahrour
    • , Maria Keays
    • , David Haussler
    • , John N. Weinstein
    • , Wolfgang Huber
    • , Alfonso Valencia
    • , Peter J. Park
    • , Irene Papatheodorou
    • , Jingchun Zhu
    • , Vincent Ferretti
    •  & Miguel Vazquez
  • Reviews
    | Open Access

    The analysis of ctDNA obtained from low-volume blood samples has the potential to transform the management of patients with colorectal cancer. Nevertheless, research priorities and minimum standards for sample collection and analysis in this area are currently missing. In this Position Paper, the NCI Colon and Rectal–Anal Task Forces provide a set of recommendations designed to address these challenges and accelerate the implementation of ctDNA in the management of patients with colorectal cancer.

    • Arvind Dasari
    • , Van K. Morris
    • , Carmen J. Allegra
    • , Chloe Atreya
    • , Al B. Benson III
    • , Patrick Boland
    • , Ki Chung
    • , Mehmet S. Copur
    • , Ryan B. Corcoran
    • , Dustin A. Deming
    • , Andrea Dwyer
    • , Maximilian Diehn
    • , Cathy Eng
    • , Thomas J. George
    • , Marc J. Gollub
    • , Rachel A. Goodwin
    • , Stanley R. Hamilton
    • , Jaclyn F. Hechtman
    • , Howard Hochster
    • , Theodore S. Hong
    • , Federico Innocenti
    • , Atif Iqbal
    • , Samuel A. Jacobs
    • , Hagen F. Kennecke
    • , James J. Lee
    • , Christopher H. Lieu
    • , Heinz-Josef Lenz
    • , O. Wolf Lindwasser
    • , Clara Montagut
    • , Bruno Odisio
    • , Fang-Shu Ou
    • , Laura Porter
    • , Kanwal Raghav
    • , Deborah Schrag
    • , Aaron J. Scott
    • , Qian Shi
    • , John H. Strickler
    • , Alan Venook
    • , Rona Yaeger
    • , Greg Yothers
    • , Y. Nancy You
    • , Jason A. Zell
    •  & Scott Kopetz

News and Comment

  • Correspondence |

    • David Tamborero
    • , Rodrigo Dienstmann
    • , Maan Haj Rachid
    • , Jorrit Boekel
    • , Richard Baird
    • , Irene Braña
    • , Luigi De Petris
    • , Jeffrey Yachnin
    • , Christophe Massard
    • , Frans L. Opdam
    • , Richard Schlenk
    • , Claudio Vernieri
    • , Elena Garralda
    • , Michele Masucci
    • , Xenia Villalobos
    • , Elena Chavarria
    • , Shubha Anand
    • , Analía Azaro
    • , Danny Baars
    • , Svetlana Bajalica-Lagercrantz
    • , Judith Balmaña
    • , Jonas Bergh
    • , Mariska Bierkens
    • , Lennart Blomqvist
    • , Gary J. Doherty
    • , Arnauld Forest
    • , Valentina Fornerone
    • , Ionut Gabriel Funingana
    • , Paola Gabaldi
    • , Johan Hartman
    • , Peter Horak
    • , Claes Karlsson
    • , Mary Kasanicki
    • , Simon Kreutzfeldt
    • , Rolf Lewensohn
    • , Johan Lindberg
    • , Carlos Lopez
    • , Andreas Lundqvist
    • , Patricia Martin-Romano
    • , Jose-Ezequiel Martin
    • , Gerrit Meijer
    • , Susana Muñoz
    • , Maud Ngo Camus
    • , Claudio Nicotra
    • , Paolo Nuciforo
    • , Petra Oberrauch
    • , Päivi Östling
    • , Alejandro Piris-Giménez
    • , Elena Provenzano
    • , Etienne Rouleau
    • , John Rowell
    • , Omar Saavedra
    • , Ignacio Sánchez Valdivia
    • , Giovanni Scoazec
    • , Kenneth Seamon
    • , Marc Tischkowitz
    • , Lizet van der Kolk
    • , Ruud van der Noll
    • , Daniel Vis
    • , Ana Vivancos
    • , Christina von Gertten
    • , Anders Wennborg
    • , Lodewyk Wessels
    • , Valtteri Wirta
    • , Julia Wolfart
    • , Fabien Calvo
    • , Stefan Fröhling
    • , Alexander Eggermont
    • , Giovanni Apolone
    • , Emile E. Voest
    • , Carlos Caldas
    • , Josep Tabernero
    • , Ingemar Ernberg
    • , Jordi Rodon
    •  & Janne Lehtiö
  • Comments and Opinion
    | Open Access

    The timing of cancer metastasis has implications for treatment and prevention. Traditional forward-time views of metastasis assume it occurs late during evolution. However, looking backward in time reveals metastasis often occurs prior to clinical detection of primary tumors.

    • Zheng Hu
    •  & Christina Curtis
  • Research Highlights |

    Normal tissues become colonized by clones, which have acquired somatic mutations in common cancer driver genes. Colom et al. have now shown that the fate of mutagen-exposed oesophageal epithelial cells in mice is governed by the genotype of their neighbours with implications for cancer development.

    • Anna Dart
  • News and Views |

    Bacteria within tumours affect progression and response to therapy; in addition, bacterial DNA can be detected in cell-free plasma. Herein, we discuss evidence showing that intratumoural bacteria are characteristic for each tumour type, and that detection of cell-free bacterial DNA in blood could provide an accurate and non-invasive test for cancer diagnosis.

    • Amiran Dzutsev
    •  & Giorgio Trinchieri
  • News and Views |

    Interleukin-8, produced by intratumoral and circulating myeloid cells, correlates with an immunosuppressive myeloid-enriched tumor microenvironment and adverse cancer prognosis.

    • Ziad Bakouny
    •  & Toni K. Choueiri
    Nature Medicine 26, 650-651