Literature DB >> 19305388

From cancer genomes to cancer models: bridging the gaps.

Anaïs Baudot1, Francisco X Real, José M G Izarzugaza, Alfonso Valencia.   

Abstract

Cancer genome projects are now being expanded in an attempt to provide complete landscapes of the mutations that exist in tumours. Although the importance of cataloguing genome variations is well recognized, there are obvious difficulties in bridging the gaps between high-throughput resequencing information and the molecular mechanisms of cancer evolution. Here, we describe the current status of the high-throughput genomic technologies, and the current limitations of the associated computational analysis and experimental validation of cancer genetic variants. We emphasize how the current cancer-evolution models will be influenced by the high-throughput approaches, in particular through efforts devoted to monitoring tumour progression, and how, in turn, the integration of data and models will be translated into mechanistic knowledge and clinical applications.

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Mesh:

Year:  2009        PMID: 19305388      PMCID: PMC2672900          DOI: 10.1038/embor.2009.46

Source DB:  PubMed          Journal:  EMBO Rep        ISSN: 1469-221X            Impact factor:   8.807


  59 in total

1.  dbSNP: the NCBI database of genetic variation.

Authors:  S T Sherry; M H Ward; M Kholodov; J Baker; L Phan; E M Smigielski; K Sirotkin
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

Review 2.  Listening to silence and understanding nonsense: exonic mutations that affect splicing.

Authors:  Luca Cartegni; Shern L Chew; Adrian R Krainer
Journal:  Nat Rev Genet       Date:  2002-04       Impact factor: 53.242

3.  A progression puzzle.

Authors:  René Bernards; Robert A Weinberg
Journal:  Nature       Date:  2002-08-22       Impact factor: 49.962

4.  Mutational analysis of the tyrosine kinome in colorectal cancers.

Authors:  Alberto Bardelli; D Williams Parsons; Natalie Silliman; Janine Ptak; Steve Szabo; Saurabh Saha; Sanford Markowitz; James K V Willson; Giovanni Parmigiani; Kenneth W Kinzler; Bert Vogelstein; Victor E Velculescu
Journal:  Science       Date:  2003-05-09       Impact factor: 47.728

5.  SIFT: Predicting amino acid changes that affect protein function.

Authors:  Pauline C Ng; Steven Henikoff
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

6.  Limits to the Human Cancer Genome Project?

Authors:  Bernard S Strauss
Journal:  Science       Date:  2007-02-09       Impact factor: 47.728

7.  Limits to the Human Cancer Genome Project?

Authors:  Wee J Chng
Journal:  Science       Date:  2007-02-09       Impact factor: 47.728

8.  p53 website and analysis of p53 gene mutations in human cancer: forging a link between epidemiology and carcinogenesis.

Authors:  T Soussi; K Dehouche; C Béroud
Journal:  Hum Mutat       Date:  2000       Impact factor: 4.878

9.  The consensus coding sequences of human breast and colorectal cancers.

Authors:  Tobias Sjöblom; Siân Jones; Laura D Wood; D Williams Parsons; Jimmy Lin; Thomas D Barber; Diana Mandelker; Rebecca J Leary; Janine Ptak; Natalie Silliman; Steve Szabo; Phillip Buckhaults; Christopher Farrell; Paul Meeh; Sanford D Markowitz; Joseph Willis; Dawn Dawson; James K V Willson; Adi F Gazdar; James Hartigan; Leo Wu; Changsheng Liu; Giovanni Parmigiani; Ben Ho Park; Kurtis E Bachman; Nickolas Papadopoulos; Bert Vogelstein; Kenneth W Kinzler; Victor E Velculescu
Journal:  Science       Date:  2006-09-07       Impact factor: 47.728

10.  From latent disseminated cells to overt metastasis: genetic analysis of systemic breast cancer progression.

Authors:  Oleg Schmidt-Kittler; Thomas Ragg; Angela Daskalakis; Martin Granzow; Andre Ahr; Thomas J F Blankenstein; Manfred Kaufmann; Joachim Diebold; Hans Arnholdt; Peter Muller; Joachim Bischoff; Detlev Harich; Gunter Schlimok; Gert Riethmuller; Roland Eils; Christoph A Klein
Journal:  Proc Natl Acad Sci U S A       Date:  2003-06-13       Impact factor: 11.205

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  16 in total

1.  Has discovery-based cancer research been a bust?

Authors:  R J Epstein
Journal:  Clin Transl Oncol       Date:  2013-09-04       Impact factor: 3.405

2.  Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor.

Authors:  Xun Xu; Yong Hou; Xuyang Yin; Li Bao; Aifa Tang; Luting Song; Fuqiang Li; Shirley Tsang; Kui Wu; Hanjie Wu; Weiming He; Liang Zeng; Manjie Xing; Renhua Wu; Hui Jiang; Xiao Liu; Dandan Cao; Guangwu Guo; Xueda Hu; Yaoting Gui; Zesong Li; Wenyue Xie; Xiaojuan Sun; Min Shi; Zhiming Cai; Bin Wang; Meiming Zhong; Jingxiang Li; Zuhong Lu; Ning Gu; Xiuqing Zhang; Laurie Goodman; Lars Bolund; Jian Wang; Huanming Yang; Karsten Kristiansen; Michael Dean; Yingrui Li; Jun Wang
Journal:  Cell       Date:  2012-03-02       Impact factor: 41.582

3.  Molecular, cellular and physiological characterization of the cancer cachexia-inducing C26 colon carcinoma in mouse.

Authors:  Paola Aulino; Emanuele Berardi; Veronica M Cardillo; Emanuele Rizzuto; Barbara Perniconi; Carla Ramina; Fabrizio Padula; Enrico P Spugnini; Alfonso Baldi; Fabio Faiola; Sergio Adamo; Dario Coletti
Journal:  BMC Cancer       Date:  2010-07-08       Impact factor: 4.430

4.  Interpretation of the consequences of mutations in protein kinases: combined use of bioinformatics and text mining.

Authors:  Jose M G Izarzugaza; Martin Krallinger; Alfonso Valencia
Journal:  Front Physiol       Date:  2012-08-22       Impact factor: 4.566

5.  Characterization of pathogenic germline mutations in human protein kinases.

Authors:  Jose M G Izarzugaza; Lisa E M Hopcroft; Anja Baresic; Christine A Orengo; Andrew C R Martin; Alfonso Valencia
Journal:  BMC Bioinformatics       Date:  2011-07-05       Impact factor: 3.169

6.  Prioritization of pathogenic mutations in the protein kinase superfamily.

Authors:  Jose M G Izarzugaza; Angela del Pozo; Miguel Vazquez; Alfonso Valencia
Journal:  BMC Genomics       Date:  2012-06-18       Impact factor: 3.969

7.  Extraction of human kinase mutations from literature, databases and genotyping studies.

Authors:  Martin Krallinger; Jose M G Izarzugaza; Carlos Rodriguez-Penagos; Alfonso Valencia
Journal:  BMC Bioinformatics       Date:  2009-08-27       Impact factor: 3.169

8.  Chapter 14: Cancer genome analysis.

Authors:  Miguel Vazquez; Victor de la Torre; Alfonso Valencia
Journal:  PLoS Comput Biol       Date:  2012-12-27       Impact factor: 4.475

Review 9.  Getting personalized cancer genome analysis into the clinic: the challenges in bioinformatics.

Authors:  Alfonso Valencia; Manuel Hidalgo
Journal:  Genome Med       Date:  2012-07-30       Impact factor: 11.117

10.  wKinMut: an integrated tool for the analysis and interpretation of mutations in human protein kinases.

Authors:  Jose M G Izarzugaza; Miguel Vazquez; Angela del Pozo; Alfonso Valencia
Journal:  BMC Bioinformatics       Date:  2013-11-29       Impact factor: 3.169

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