Bladder Cancer - Invasive Urothelial Bladder Cancer 
Bone Cancer - Osteosarcoma / chondrosarcoma / rare subtypes 
Breast Cancer - Ductal carcinoma 
Breast cancer - Asian phenotype 
Pediatric Brain Tumors - Medulloblasma & Pediatric Pilocytic Astrocytoma 
Brain Cancer - Pediatric Medulloblastoma 
Colorectal cancer - Adenocarcinoma, non-Western 
Oral Cancer - Gingivobuccal 
Thyroid Cancer - Papillary thyroid carcinoma 
Chronic Lymphocytic Leukemia - CLL with mutated and unmutated IgVH 
Liver Cancer - Hepatocellular carcinoma (Virus associated) 
Ovarian Cancer - Serous cystadenocarcinoma 
Rare Pancreatic Tumors - Enteropancreatic endocrine tumors and rare pancreatic exocrine tumors 
| European Commission: | European Commission FP7 |
| Czech Republic: | Institute of Hygiene and Epidemiology, First Faculty of Medicine, Charles University of Prague |
| France: | Centre National de Génotypage (CNG) |
| International Agency for Research on Cancer (IARC) | |
| Russian Federation: | N. N. Blokhin Russian Cancer Research Centre and Russian Cancer Society |
| Sweden: | Karolinska Institute |
| Karolinska University Hospital | |
| United Kingdom: | Cancer Research UK Centre, University of Leeds |
Samples with sufficient frozen tissue for subsequent genetic/epigenetic analysis will be reviewed independently and consensus histopathological diagnosis agreed by 3 pathologists. Digital images will be captured and stored for reference purposes with annotation from the pathologists. Using FFPE tissue sections, tumours will be subtyped using the WHO classification and staged using the 2002 TNM system. Conventional/clear cell renal carcinoma shows a spectrum of morphology ranging from pure clear cell through varying proportions of clear versus granular (mitochondria-rich) cells and the relative proportions will be recorded for each tumour. In each case where there is diagnostic difficulty, either for the identification of translocation-associated tumours or in the distinction between eosinophilic tumour subtypes, immunocytochemistry will be performed. Tumours will be graded using both the Fuhrmann and Mayo clinic system. The samples from the non-conventional/clear cell RCC subtypes will also be similarly characterised and made available for use in the project.
| France: | Centre National de Génotypage (CNG) |
| Fondation Jean Dausset, Centre d’Etude du Polymorphisme Humain (CEPH) | |
| Russian Federation: | Center BioEngineering, Russian Academy of Sciences |
| Kurchatov Scientific Center |
Technology platform:
Illumina/SOLEXA
Full genome sequencing (matched blood and tumor)
Transcriptome profiling in peri-tumoral and tumoral tissue
(RNA-seq)
Methylation profiling in peri-tumoral and tumoral tissue
(MeDIP or MBD-seq)
| France: | Centre National de Génotypage (CNG) |
| Fondation Jean Dausset, Centre d’Etude du Polymorphisme Humain (CEPH) | |
| Russian Federation: | Center BioEngineering, Russian Academy of Sciences |
| Kurchatov Scientific Center |
Follow-up studies of identified genetic, transcriptomic and epgenetic differences in up to 1500 samples.
| France: | Centre National de Génotypage (CNG) |
| Fondation Jean Dausset, Centre d’Etude du Polymorphisme Humain (CEPH) | |
| Latvia: | Institute of Mathematics and Computer Science, University of Latvia |
| United Kingdom: | European Bioinformatics Institute |
The pre-processed data, summary data and the appropriate sample/phenotype data will be transferred to the European Bioinformatics Institute, where it will be stored in the permanent data repositories. In particular short read sequence data will be deposited into the European Short Read Archive (ESRA). The appropriate sample/phenotype data will be stored into a central sample index at EBI, with links to the respective assay data. The data release will be controlled by the depositors and the consortium agreement. The archived data will be linked to the respective added value databases, such as the Ensembl genome browser, the ArrayExpress Atlas of Gene Expression, and Reactome pathway database.
The CAGEKID consortium is performing a comprehensive investigation of genetic and epigenetic changes and resultant downstream proteomic changes in the most common form of renal cancer, renal cell carcinoma (RCC). RCC accounts for approximately 85% of all cases. Malignant renal tumours constitute 3% of human cancers, although their frequency differs greatly in various areas higher incidence rates are for example found in eastern and central Europe where the incidence of renal cancers has been increasing since the 1950s. Identified etiological risk factors include smoking, increased body mass, dietary factors and chronic renal disease. RCC is asymptomatic and there are no biological markers available for diagnostic, prognostic and predictive purpose. Several types of cancer can develop in the kidneys. Despite the introduction of several new treatment modalities in the last years, renal carcinoma - similarly to pancreatic carcinoma - are characterized by a low sensitivity to chemotherapy and radiotherapy. The project will yield new biological markers that will give better understanding of the disease aetiology, provide new diagnostic and prognostic tools, and lead to new therapies.
Fondation Jean Dausset, Centre d’Etude du Polymorphisme Humain (CEPH), France
• Mark Lathrop
• Jörg Tost
International Agency for Research on Cancer, France
• Paul Brennan
Institute of Hygiene and Epidemiology, First Faculty of Medicine, Charles University of Prague, Czech Republic
• Ivana Holcatova
Department of Epidemiology and Prevention, Russian N.N.Blokhin Cancer Research Centre and Russian Cancer Society, Russian Federation
• David Zaridze
European Molecular Biology Laboratory, European Bioinformatics Institute, United Kingdom
• Alvis Brazma
Karolinska Institute/ Karolinska University Hospital, Sweden
• Lars Egevad
Center BioEngineering, Russian Academy of Sciences, Russian Federation
• Egor Prokhortchouk
Cancer Research UK Centre, University of Leeds, United Kingdom
• Rosamonde Elizabeth Banks
Royal Institute of Technology, Sweden
• Mathias Uhlén
Centre National de Génotypage, Institut Génomique, Commissariat à l'Energie Atomique, France
• Mark Lathrop
• Jörg Tost
Institut National de la Sante et de la Recheche Medicale, France
• Anne Cambon-Thomsen
Institute of Mathematics and Computer Science, Latvia
• Juris Viksna
Uppsala University, Sweden
• Fredrik Ponten
Kurchatov Scientific Center, Russian Federation
• Konstantin Skryabin