The Cancer Genome Atlas

The Cancer Genome Atlas (TCGA) is a project to catalogue the genetic mutations responsible for cancer using genome sequencing and bioinformatics. The overarching goal was to apply high-throughput genome analysis techniques to improve the ability to diagnose, treat, and prevent cancer through a better understanding of the genetic basis of the disease. TCGA was supervised by the National Cancer Institute's Center for Cancer Genomics and the National Human Genome Research Institute funded by the US government. A three-year pilot project, begun in 2006, focused on characterization of three types of human cancers: glioblastoma multiforme, lung squamous carcinoma, and ovarian serous adenocarcinoma. In 2009, it expanded into phase II, which planned to complete the genomic characterization and sequence analysis of 20–25 different tumor types by 2014. Ultimately, TCGA surpassed that goal, characterizing 33 cancer types including 10 rare cancers. The project initially set out to collect and ch

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BIO-471: Cancer biology I

The course covers in detail molecular mechanisms of cancer development with emphasis on cell cycle control, genome stability, oncogenes and tumor suppressor genes.

BIOENG-420: Single cell biology

The students are exposed to experimental and analytical approaches specific to single cell biology, with an emphasis on quantitative aspects.

Molecular characterization of dormant and activated hematopoietic stem cells

Robin Graf

2010

Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies

Elena Battistello, Giovanni Ciriello, Titouan Laessle, Marco Mina, Elisa Oricchio, Franck Claude Raynaud, Mohammad Sadegh Saghafinia, Stephanie Jocelyne Sungalee

Cancer evolves through the emergence and selection of molecular alterations. Cancer genome profiling has revealed that specific events are more or less likely to be co-selected, suggesting that the selection of one event depends on the others. However, the nature of these evolutionary dependencies and their impact remain unclear. Here, we designed SELECT, an algorithmic approach to systematically identify evolutionary dependencies from alteration patterns. By analyzing 6,456 genomes from multiple tumor types, we constructed a map of oncogenic dependencies associated with cellular pathways, transcriptional readouts, and therapeutic response. Finally, modeling of cancer evolution shows that alteration dependencies emerge only under conditional selection. These results provide a framework for the design of strategies to predict cancer progression and therapeutic response.

Cell Press2017

MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data

Bryan Alexander Ford, Joao André Gomes de Sá E Sousa, Jean-Pierre Hubaux, Olivier Michielin, Mickaël Misbach, Jean Louis Raisaro, Juan Ramón Troncoso-Pastoriza

The increasing number of health-data breaches is creating a complicated environment for medical-data sharing and, consequently, for medical progress. Therefore, the development of new solutions that can reassure clinical sites by enabling privacy-preserving sharing of sensitive medical data in compliance with stringent regulations (e.g., HIPAA, GDPR) is now more urgent than ever. In this work, we introduce MedCo, the first operational system that enables a group of clinical sites to federate and collectively protect their data in order to share them with external investigators without worrying about security and privacy concerns. MedCo uses (a) collective homomorphic encryption to provide trust decentralization and end-to-end confidentiality protection, and (b) obfuscation techniques to achieve formal notions of privacy, such as differential privacy. A critical feature of MedCo is that it is fully integrated within the i2b2 (Informatics for Integrating Biology and the Bedside) framework, currently used in more than 300 hospitals worldwide. Therefore, it is easily adoptable by clinical sites. We demonstrate MedCo’s practicality by testing it on data from The Cancer Genome Atlas in a simulated network of three institutions. Its performance is comparable to the ones of SHRINE (networked i2b2), which, in contrast, does not provide any data protection guarantee.

2019

Ovarian cancer

Ovarian cancer is a cancerous tumor of an ovary. It may originate from the ovary itself or more commonly from communicating nearby structures such as fallopian tubes or the inner lining of the abdome

Carcinogenesis

Carcinogenesis, also called oncogenesis or tumorigenesis, is the formation of a cancer, whereby normal cells are transformed into cancer cells. The process is characterized by changes at the cellular

Proteomics

Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of