News from CEXS-UPF
Cancer is a heterogeneous disease at the molecular level to the clinical level. However, the technology allows to characterize the tumor cells to a level of unprecedented detail and the challenge now is to make sense of this vast amount of information to understand the biology of tumor genesis and especially to determine the most effective treatments for each patient.
To this end, the Cancer Genome Atlas Research Network, an initiative of the National Cancer Institute and the National Human Genome Research Institute of the United States was created in order to identify molecular profiles - genome, epigenome and transcriptome - of a thousand tumors of cancers that are more prevalent in the population.
Nuria Lopez-Bigas, along with Abel Gonzalez-Perez and David Tamborero, researchers and director of the Biomedical Genomics laboratory at CEXS-UPF respectively, have collaborated on this project through the analysis of mutations present in tumor tissues (mainly lung, breast, bladder and brain) to identify, among all the observed changes, which are really key to the development and progression of each tumor.
In recent years, the research group led by Nuria Lopez-Bigas has been working on the development of two methods - oncodriveCLUST and oncodriveFM - and studying positive selection signals that characterize alterations that support the behavior of cancer. Positive selection in the context of cancer is fixing alterations that confer a competitive advantage during tumor evolution.
UPF press release (in Catalan)
Cancer Genome Atlas Research Network, John N. Weinstein, Eric A. Collison, Gordon B. Mills, Kenna M. Shaw, Brad A. Ozenberger, Kyle Ellrot, Ilya Shmulevich, Chris Sander, Joshua M. Stuart, et. al. (2013), "The Cancer Genome Atlas Pan-Cancer Analysis Project", Nature Genetics, 26 de setembre.
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A & Lopez-Bigas N. (2013), "IntOGen-mutations identifies cancer drivers across tumor types", Nature Methods, 15 de setembre, doi:10.1038/nmeth.2642.
Gonzalez-Perez A.; Jene-Sanz A. i Lopez-Bigas N. (2013), "The mutational landscape of chromatin regulatory factors across 4623 tumor samples", Genome Biology, 25 de setembre, doi:10.1186/gb-2013-14-9-r106.
David Tamborero, Abel Gonzalez-Perez, Christian Perez-Llamas, Jordi Deu-Pons, Cyriac Kandoth, Jüri Reimand, Michael S. Lawrence, Gad Getz, Gary D. Bader, Li Ding i Nuria Lopez-Bigas (2013), "Comprehensive identification of mutational cancer driver genes across 12 tumor types", Scientific Reports, 26 de setembre, DOI: 10.1038/srep02650.