Integrative Cancer Genomics

   Deadline for applications: October 13th 2010
        EARLY: September 16th 2010
        NORMAL: October 16th 2010
   Course date: November 8th - November 10th 2010


Nuria Lopez-Bigas is the head of the Biomedical Genomics group at the Universitat Pompeu Fabra (UPF) in Barcelona. She completed her PhD degree on 2002 on the molecular basis of deafness at the Oncologic Research Institute in Barcelona. She then moved to the European Bioinformatics Institute in Hinxton (Cambridge, UK) to initiate a project on the computational study of disease and cancer genes. Since 2006 is a group leader at the UPF focusing on cancer genomics and bioinformatics.
Universitat Pompeu Fabra (UPF), Barcelona, Spain

Gunes Gundem has a Master in Computational Science and Engineering from Koc University (Istanbul, Turkey) and a Molecular Biology and Genetics degree from the Middle East Technical University (Ankara, Turkey). She is currently a last year PhD student at the Biomedical Genomics group of the Universidad Pompeu Fabra. She is mainly interested in translational oncogenomics, which analyzes and integrates large-scale, heterogeneous data in order to gain biological insights with potential clinical application.
Universitat Pompeu Fabra (UPF), Barcelona, Spain

Course description:

In the last few years, the study of the genetic basis of cancer has undergone a profound transformation. High-throughput techniques, such as microarrays and next generation sequencing technologies, allow scientists to identify genetic alterations at genome-wide level in many tumour types. The application of these technologies to the study of cancer is very powerful to understand the mechanism of disease pathogenesis, and it has a high potential to identify possible targets for therapy, discover molecular biomarkers that allow an early detection of cancer, improve the diagnosis and prognosis or certain tumours, and predict the response to therapies. The application of these technologies yields complex, multidimensional genomic data sets that describe in detail the myriad changes that occur within individual tumours and how these changes differ between individual tumours. As a consequence, modern cancer research has become a hybrid of molecular and bioinformatic methods. The course will provide the students with theoretical and practical expertise in the field of integrative cancer genomics. We will introduce the large oncogenomic projects that are active, such as The Cancer Genome Atlas[1] and the International Cancer Genome Consortium[2]. And we will learn how to use tools to access, manipulate and take advantage of the large amount of available cancer genomics data. Some tools we will use are IntOGen[3], Oncomine[4], COSMIC[5], ICGC-DCC [2] and MEV among others.

Target Audience

The course is directed to researchers in biology and medicine. Background knowledge in bioinformatics is not necessary. Attendees will be updated on the state of the art in the field of cancer genomics and they will become capable of handling and analyzing cancer genomics data. Upon completion, the atendees will be able to perform integrative analysis and interpret the results, in order to answer specific biological questions.


1. TCGA. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061-1068 (2008).
2. ICGC. International network of cancer genome projects. Nature 464, 993-998 (2010).
3. Gundem, G. et al. IntOGen: integration and data mining of multidimensional oncogenomic data. Nat. Methods 7, 92-93 (2010).
4. Rhodes, D.R. et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9, 166-180 (2007).
5. Forbes, S.A. et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res 38, D652-657 (2010).
Course Pre-requisites:

Basic Molecular Biology. Elementary computing skills.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  August 1st 2010