Literature DB >> 20161678

Next-generation sequencing of cancer genomes: back to the future.

Matthew J Walter, Timothy A Graubert, John F Dipersio, Elaine R Mardis, Richard K Wilson, Timothy J Ley.   

Abstract

The systematic karyotyping of bone marrow cells was the first genomic approach used to personalize therapy for patients with leukemia. The paradigm established by cytogenetic studies in leukemia (from gene discovery to therapeutic intervention) now has the potential to be rapidly extended with the use of whole-genome sequencing approaches for cancer, which are now possible. We are now entering a period of exponential growth in cancer gene discovery that will provide many novel therapeutic targets for a large number of cancer types. Establishing the pathogenetic relevance of individual mutations is a major challenge that must be solved. However, after thousands of cancer genomes have been sequenced, the genetic rules of cancer will become known and new approaches for diagnosis, risk stratification and individualized treatment of cancer patients will surely follow.

Entities:  

Year:  2009        PMID: 20161678      PMCID: PMC2821057          DOI: 10.2217/pme.09.52

Source DB:  PubMed          Journal:  Per Med        ISSN: 1741-0541            Impact factor:   2.512


  48 in total

1.  ChIP-seq: welcome to the new frontier.

Authors:  Elaine R Mardis
Journal:  Nat Methods       Date:  2007-08       Impact factor: 28.547

2.  Characteristic chromosomal abnormalities in biopsies and lymphoid-cell lines from patients with Burkitt and non-Burkitt lymphomas.

Authors:  L Zech; U Haglund; K Nilsson; G Klein
Journal:  Int J Cancer       Date:  1976-01-15       Impact factor: 7.396

3.  High meningioma 1 (MN1) expression as a predictor for poor outcome in acute myeloid leukemia with normal cytogenetics.

Authors:  Michael Heuser; Gernot Beutel; Juergen Krauter; Konstanze Döhner; Nils von Neuhoff; Brigitte Schlegelberger; Arnold Ganser
Journal:  Blood       Date:  2006-08-15       Impact factor: 22.113

4.  Haploinsufficiency of CBFA2 causes familial thrombocytopenia with propensity to develop acute myelogenous leukaemia.

Authors:  W J Song; M G Sullivan; R D Legare; S Hutchings; X Tan; D Kufrin; J Ratajczak; I C Resende; C Haworth; R Hock; M Loh; C Felix; D C Roy; L Busque; D Kurnit; C Willman; A M Gewirtz; N A Speck; J H Bushweller; F P Li; K Gardiner; M Poncz; J M Maris; D G Gilliland
Journal:  Nat Genet       Date:  1999-10       Impact factor: 38.330

5.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

6.  Mutation of CEBPA in familial acute myeloid leukemia.

Authors:  Matthew L Smith; Jamie D Cavenagh; T Andrew Lister; Jude Fitzgibbon
Journal:  N Engl J Med       Date:  2004-12-02       Impact factor: 91.245

7.  High EVI1 levels predict adverse outcome in acute myeloid leukemia: prevalence of EVI1 overexpression and chromosome 3q26 abnormalities underestimated.

Authors:  Sanne Lugthart; Ellen van Drunen; Yvette van Norden; Antoinette van Hoven; Claudia A J Erpelinck; Peter J M Valk; H Berna Beverloo; Bob Löwenberg; Ruud Delwel
Journal:  Blood       Date:  2008-02-13       Impact factor: 22.113

Review 8.  Leukemia and lymphoma in ataxia telangiectasia.

Authors:  A M Taylor; J A Metcalfe; J Thick; Y F Mak
Journal:  Blood       Date:  1996-01-15       Impact factor: 22.113

9.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Authors:  Gordon Robertson; Martin Hirst; Matthew Bainbridge; Misha Bilenky; Yongjun Zhao; Thomas Zeng; Ghia Euskirchen; Bridget Bernier; Richard Varhol; Allen Delaney; Nina Thiessen; Obi L Griffith; Ann He; Marco Marra; Michael Snyder; Steven Jones
Journal:  Nat Methods       Date:  2007-06-11       Impact factor: 28.547

Review 10.  The cancer genome.

Authors:  Michael R Stratton; Peter J Campbell; P Andrew Futreal
Journal:  Nature       Date:  2009-04-09       Impact factor: 49.962

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  9 in total

Review 1.  Genomic tools in acute myeloid leukemia: From the bench to the bedside.

Authors:  Brian S White; John F DiPersio
Journal:  Cancer       Date:  2014-01-28       Impact factor: 6.860

Review 2.  Mutational analysis of breast cancer: guiding personalized treatments.

Authors:  Matthew J Ellis
Journal:  Breast       Date:  2013-08       Impact factor: 4.380

Review 3.  An integrated genomic approach to the assessment and treatment of acute myeloid leukemia.

Authors:  Lucy A Godley; John Cunningham; M Eileen Dolan; R Stephanie Huang; Sandeep Gurbuxani; Megan E McNerney; Richard A Larson; Hoyee Leong; Yves Lussier; Kenan Onel; Olatoyosi Odenike; Wendy Stock; Kevin P White; Michelle M Le Beau
Journal:  Semin Oncol       Date:  2011-04       Impact factor: 4.929

4.  Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression.

Authors:  Lukas D Wartman; David E Larson; Zhifu Xiang; Li Ding; Ken Chen; Ling Lin; Patrick Cahan; Jeffery M Klco; John S Welch; Cheng Li; Jacqueline E Payton; Geoffrey L Uy; Nobish Varghese; Rhonda E Ries; Mieke Hoock; Daniel C Koboldt; Michael D McLellan; Heather Schmidt; Robert S Fulton; Rachel M Abbott; Lisa Cook; Sean D McGrath; Xian Fan; Adam F Dukes; Tammi Vickery; Joelle Kalicki; Tamara L Lamprecht; Timothy A Graubert; Michael H Tomasson; Elaine R Mardis; Richard K Wilson; Timothy J Ley
Journal:  J Clin Invest       Date:  2011-03-23       Impact factor: 14.808

Review 5.  Are results of targeted gene sequencing ready to be used for clinical decision making for patients with acute myelogenous leukemia?

Authors:  Arati V Rao; B Douglas Smith
Journal:  Curr Hematol Malig Rep       Date:  2013-06       Impact factor: 3.952

6.  The Future of Children's Health in the Genomic Era.

Authors:  Alan L Schwartz
Journal:  Rambam Maimonides Med J       Date:  2011-07-31

7.  Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era.

Authors:  Robert Alan Edwards; John Matthew Haggerty; Noriko Cassman; Julia Christine Busch; Kristen Aguinaldo; Sowmya Chinta; Meredith Houle Vaughn; Robert Morey; Timothy T Harkins; Clotilde Teiling; Karin Fredrikson; Elizabeth Ann Dinsdale
Journal:  BMC Genomics       Date:  2013-09-04       Impact factor: 3.969

Review 8.  Molecular Subtyping of Pancreatic Cancer: Translating Genomics and Transcriptomics into the Clinic.

Authors:  Yongxing Du; Bangbo Zhao; Ziwen Liu; Xiaoxia Ren; Wenjing Zhao; Zongze Li; Lei You; Yupei Zhao
Journal:  J Cancer       Date:  2017-02-11       Impact factor: 4.207

9.  Duplex sequencing identifies genomic features that determine susceptibility to benzo(a)pyrene-induced in vivo mutations.

Authors:  Danielle P M LeBlanc; Matthew Meier; Fang Yin Lo; Elizabeth Schmidt; Charles Valentine; Andrew Williams; Jesse J Salk; Carole L Yauk; Francesco Marchetti
Journal:  BMC Genomics       Date:  2022-07-28       Impact factor: 4.547

  9 in total

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