TY - JOUR
T1 - Getting personalized cancer genome analysis into the clinic
T2 - the challenges in bioinformatics
AU - Valencia, Alfonso
AU - Hidalgo, Manuel
N1 - Funding Information:
The work in the group of AV related to this review is supported by grants from the ENCODE Project (U54 HG0004555), eTOX (Grant 115002, Innovative Medicines Initiative) and Consolider E-Science (CSD2007-00050), the Instituto de Salud Carlos III COMBIOMED (RD07/0067/0014) and the Spanish Ministry of Science and Innovation (BIO2007-66855). MH’s work is supported by grants from the Spanish FIS (PI10/01996) and USA National Cancer Institute (1R01-CA129963). The assistance provided by the Spanish Bioinformatics Institute (INB), a platform of the ISCII, is particularly appreciated. We are indebted to David G Pisano, Miguel Vazquez, Victor de la Torre, Gonzalo Gomez, Enrique Carrillo, Francisco Real, Jose MG Izarzugaza, Anäis Buadot, Enrico Glaab, Michael Tress, Daniel Rico, David de Juan for interesting discussions and insights.
PY - 2012/7/30
Y1 - 2012/7/30
N2 - Progress in genomics has raised expectations in many fields, and particularly in personalized cancer research. The new technologies available make it possible to combine information about potential disease markers, altered function and accessible drug targets, which, coupled with pathological and medical information, will help produce more appropriate clinical decisions. The accessibility of such experimental techniques makes it all the more necessary to improve and adapt computational strategies to the new challenges. This review focuses on the critical issues associated with the standard pipeline, which includes: DNA sequencing analysis; analysis of mutations in coding regions; the study of genome rearrangements; extrapolating information on mutations to the functional and signaling level; and predicting the effects of therapies using mouse tumor models. We describe the possibilities, limitations and future challenges of current bioinformatics strategies for each of these issues. Furthermore, we emphasize the need for the collaboration between the bioinformaticians who implement the software and use the data resources, the computational biologists who develop the analytical methods, and the clinicians, the systems' end users and those ultimately responsible for taking medical decisions. Finally, the different steps in cancer genome analysis are illustrated through examples of applications in cancer genome analysis.
AB - Progress in genomics has raised expectations in many fields, and particularly in personalized cancer research. The new technologies available make it possible to combine information about potential disease markers, altered function and accessible drug targets, which, coupled with pathological and medical information, will help produce more appropriate clinical decisions. The accessibility of such experimental techniques makes it all the more necessary to improve and adapt computational strategies to the new challenges. This review focuses on the critical issues associated with the standard pipeline, which includes: DNA sequencing analysis; analysis of mutations in coding regions; the study of genome rearrangements; extrapolating information on mutations to the functional and signaling level; and predicting the effects of therapies using mouse tumor models. We describe the possibilities, limitations and future challenges of current bioinformatics strategies for each of these issues. Furthermore, we emphasize the need for the collaboration between the bioinformaticians who implement the software and use the data resources, the computational biologists who develop the analytical methods, and the clinicians, the systems' end users and those ultimately responsible for taking medical decisions. Finally, the different steps in cancer genome analysis are illustrated through examples of applications in cancer genome analysis.
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U2 - 10.1186/gm362
DO - 10.1186/gm362
M3 - Review article
C2 - 22839973
AN - SCOPUS:84864185889
SN - 1756-994X
VL - 4
JO - Genome Medicine
JF - Genome Medicine
IS - 8
M1 - 61
ER -