The BASIS project is a collaboration between the following institutions and organisations:

Wellcome Trust Sanger Institute

Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute (WTSI), Hinxton, Cambridge, UK is a not-for-profit research organisation dedicated to the sequencing and functional analysis of genomes. The Sanger Institute underpins biological and medical research worldwide through large-scale analysis, focused research and collaborations. It currently has the greatest sequencing capacity of any academic institution in Europe, through considerable investment in high throughput sequencing technologies (40 second-generation sequencing machines spanning three commercially available platforms). Genome sequence analysis is complemented by computational interpretation and experimental analysis of gene function in a variety of model organisms. There are designated teams for library preparation, sequencing production and data processing. The data centre and computation and data distribution distribution is continually being extended and upgraded, and now has at least 8000 terabytes (Tb) of storage space available and computer farm consisting of over 8000 CPUs. The Cancer Genome Project at WTSI has pioneered the development of high-throughput approaches to identifying somatic variants in cancer. It has extensive experience with the application of new sequencing technologies to the annotation of cancer genomes through completion of proof-of-principle studies for identification of point mutations, copy number changes and rearrangements to the base-pair level in cancer, studying subclonal diversity in cancer and sequencing a number of whole cancer genomes. It has discovered a number of new cancer genes and patterns of somatic mutation.

Key Staff

  • Professor Michael Stratton

Contact details

Wellcome Trust Sanger Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SA

Oslo University Hospital

Oslo University Hospital

Oslo University Hospital HF (OUS), Oslo, Norway has a Comprehensive Cancer Centre (CCC) with considerable resources and extensive activity both within clinical research (The Radiumhospital and the Cancer clinic at Ullevål Hospital), basic research performed at the Institute for Cancer Research (ICR), and epidemiological/preventive cancer research (The Cancer Registry of Norway). Connected to the CCC is the Oslo Cancer Cluster (OCC) with status as a Norwegian Centre of Expertise. OCC is a non-profit member organization committed to improve the lives of cancer patients by accelerating the development of new cancer diagnostics and medicines. OUS's CCC has multiregional and nationwide functions with regards to groups of patients with rare tumours, which call for special competence. The Department of Genetics at the ICR is among the leading laboratories in research on molecular biology of breast cancer and has extensive collaboration with many international groups. Ongoing research focuses on more fundamental understanding of the biological dynamics of breast cancer using high-throughput molecular data at multiple levels (e.g. DNA, mRNA, miRNA and protein level). Various molecular profiles have been associated with tumour aggressiveness, response to therapy and patient outcome.

Key Staff

  • Prof. Anne-Lise Børresen-Dale
  • Dr Anita Langerød

Contact details

Oslo University Hospital
P. O. Box 4950 Nydalen,
N-0424 Oslo
Norway

Academisch Medisch Centrum bij de Universiteit van Amsterdam

Academisch Medisch Centrum bij de Universiteit van Amsterdam

The Academic Medical Center (AMC) in Amsterdam is a large and renowned university medical center with a long-standing tradition in clinical as well as translation cancer research. The department of Pathology has a large and well equipped research and histopathology laboratory that includes a large frozen tissue bank. The research laboratory and histopathology laboratory are well integrated and has a well established infrastructure for translational research.

Key Staff

  • Professor Marc van de Vijver

Contact details

Academisch Medisch Centrum bij de Universiteit
Postbus 22660
1100 DD Amsterdam

Radboud Universiteit Nijmegen Stichting Katholieke Universiteit

Radboud Universiteit Nijmegen Stichting Katholieke Universiteit

Radboud University, Nijmegen, The Netherlands. Research in the Department of Molecular Biology at the Nijmegen Center for Molecular Life Sciences (NCMLS) focuses on the regulation of gene transcription and chromatin remodeling in normal and deregulated cells. The research aims at deciphering the transcription factor networks and epigenetic mechanisms of gene regulation during development, differentiation and in cancer. The objectives are to unravel the mechanisms and transcription factor networks as well as the role of chromatin in development differentiation and disease. The department is performing high throughput Chip-seq, DNAme-seq and RNA-seq profiling that allow global identification and characterization of genomic target sites and transcripts on a 'routine' basis. Current genome wide profiling includes histone modifications in ES cells, DNA methylation in primary cancer and ES cells, nuclear hormone receptors, the tumor suppressor gene p53 and family members, oncogenic translocation fusion proteins in acute myeloid leukemia and synovial sarcoma, the tumor antigen PRAME and methyl-CpG binding proteins in reading and 'translating' DNA methylation. The department has acquired an Illumina platform with paired-end module. The department also has bioinformatics group that performs the data management, data visualization, peak extraction, statistical analysis and bioinformatic data mining.

Key Staff

  • Professor Henk Stunnenberg

Contact details

Radbourg University
P.O. Box 9102
6500 HC Nijmegen
The Netherlands

Cancer Research UK

Cancer Research UK

The Cancer Research UK Cambridge Research Institute (CRI), Cambridge, UK aims to link the laboratory to the clinic and emphasizes a multi-disciplinary approach to cancer-focused research. CRI is firmly embedded in the academic and research community of Cambridge University. CRI aims to be the focus for the practical application of high-quality basic research, forming a bridge between the world-class science of the University of Cambridge and its environment, and the Addenbrooke's Hospital. The Institute is also the nucleus of the wider virtual Cambridge Cancer Centre. This virtual Centre will bring together research groups from many disciplines (including for example, chemistry, mathematics and physics) across the University and local biotechnology companies under one umbrella to work on cross-disciplinary projects and share resources.

Key Staff

  • Professor Carlos Caldas

Contact details

Cancer Research UK Cambridge Research Institute
Li Ka Shing Centre
Robinson Way
Cambridge,
UK - CB2 0RE

European Molecular Biology Laboratory - European Bioinformatics Institute

European Molecular Biology Laboratory - European Bioinformatics Institute

The European Bioinformatics Institute (EBI), Cambridge, UK, is a non-profit academic organisation that forms part of the European Molecular Biology Laboratory (EMBL). The EBI is a world-renowned centre for research and services in bioinformatics and is the European node for globally coordinated efforts to collect and disseminate biological data. The EBI has the infrastructure and resources to provide large biological databases, and manages databases including nucleic acid and protein sequences and macromolecular structures. Its mission is to ensure that the growing body of information from molecular biology and genome research is placed in the public domain and is accessible freely to all facets of the scientific community in ways that promote scientific progress.

Key Staff

  • Dr Ewan Birney

Contact details

European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

Erasmus Universitair Medisch Centrum Rotterdam

Erasmus Universitair Medisch Centrum Rotterdam

The Erasmus Medical Center (EMC), Rotterdam, The Netherlands is a renowned medical center specializing in the detection and treatment of cancer with a long-standing tradition in clinical as well translation cancer research. The research section Translational Cancer Genomics and Proteomics of the department of Medical Oncology aims to investigate, using a wide variety of genomics and proteomics tools, the cell biological factors involved in the progression and treatment failure of breast cancer. The research group at EMC has amongst others a well-recognized track record on gene expression profiling leading to the identification of gene signatures associated with prognosis, response to therapy and organ-specific relapse. All expertise, including quality controlled sample preparation, actual transcriptome analysis as well as bioinformatic data analysis, is available in the laboratory.

Key Staff

  • Professor John Foekens
  • Professor den Bakker
  • Dr John Martens
  • Dr Anieta Sieuwerts
  • Dr Stefan Sleijfer

Contact details

Erasmus Medical Center
Postbus 2040
3000 CA Rotterdam

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute

The Dana-Farber Cancer Institute (DFCI), Cambridge, Massachusetts, USA. The mission of the Dana-Farber Cancer Institute is to provide expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. The DFCI occupies five adjoining buildings at the corner of Longwood and Brookline Avenues in Boston, next to Brigham and Women's Hospital, Beth Israel Deaconess Medical Center, Children's Hospital Boston, and Harvard Medical School. The DFCI is the lead institution in the Dana-Farber/Harvard Cancer Center (DF/HCC) and is a National Cancer Institute (NCI)-designated Comprehensive Cancer Center.

Key Staff

  • Dr Andrea Richardson

Contact details

Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115

Jules Bordet Institute

Jules Bordet Institute

Association Hospitaliere de Bruxelles - Centre Hospitalier Universitaire Bordet (IJB), Brussels, Belgium is an autonomous comprehensive cancer centre devoted entirely to the fight against cancer. The institution is connected with two important hospital networks: it is the anticancer centre of the University; Libre de Bruxelles (ULB) and is part of IRIS, the network of public hospitals in Brussels. Everyday, more than 115 physicians and 600 other individuals join efforts to screen and treat men and women from all social strata suffering from cancer, to perform clinical, translational and basic research, and to disperse their expertise around the world through educational programmes, lectures, and publications.

Key Staff

  • Professor Martine J. Piccart-Gebhart
  • Professor Christos Sotiriou
  • Dr Christine Desmedt

Contact details

Association Hospitaliere de Bruxelles
121 Boulevard de Waterloo,
Bruxelles 1000

The Institute of Cancer Research: Royal Cancer Hospital

The Institute of Cancer Research: Royal Cancer Hospital

The Institute of Cancer Research (ICR), London, UK is a College of the University of London and, in association with the Royal Marsden NHS Foundation Trust, forms the largest comprehensive cancer centre in Europe, and one of the largest in the world, with an outstanding national and international reputation for excellence. The quality of the research was affirmed by the UK Higher Education Funding Councils' Research Assessment Exercise in 2008 in which educational organisations' research was given a 1 to 4 star rating, with the ICR receiving the highest percentage of research assessed as world-leading (4 star rating) in the areas of biological sciences and cancer studies. The work of the ICR ranges from basic laboratory research in molecular and cell biology, biochemistry, cancer genetics, radiation physics, and drug development, through to clinical trials involving cancer patients, healthcare research and epidemiological studies in the human population. Many of the Sections undertake translational work, across the boundary between the ICR and the Royal Marsden NHS Foundation Trust, allowing projects to gain from the opportunities presented by a major comprehensive cancer centre.

Key Staff

  • Dr Jorge Reis-Filho

Contact details

Institute of Cancer Research
123 Old Brompton Road
London SW7 3RP

Lunds Universitet

Lunds Universitet

Lund University (LU), Lund, Sweden. LU is one of Northern Europe's largest institutions for Research and Higher Education. The Department of Oncology, at Lund University Hospital, is the central oncology clinic in the Southern Sweden Health Care Region, with a clinical trial unit, regional cancer registry and oncogenetic clinic for familial cancer counselling. The department has a strong preclinical and experimental breast cancer research focus, and has large resources of fresh frozen tumor tissue and blood samples from patients with clinical follow-up available for retroactive studies. The clinical laboratory is responsible for mutation screening and testing in familial breast cancer in Sweden. The research laboratory manages the SCIBLU Genomics microarray resource center (www.lth.se/sciblu2/genomics_services), providing access to and service for all major microarray platforms, as well as database and data analysis program development (http://base.thep.lu.se).

Key Staff

  • Professor Åke Borg
  • Mr Johan Staaf

Contact details

Lund University
Box 117,
221 00 Lund,
Sweden

Institut National du Cancer

Institut National du Cancer

The Institut National du Cancer (INCa), France is the French national health care and science agency dedicated to oncology. It was created to enable a long-lasting, coordinated national policy against cancer. Placed under the tutelage of the Ministries of Health and Research, it brings together all the stakeholders involved in the fight against cancer in France. The missions of INCa encompass public health and epidemiology, basic and translational research, quality of care and information dedicated to patients and professionals. These missions provide the rationale for its leading role in large, nationwide initiatives. Its annual budget to support research activities amounts to 60 M € / year. INCa acts through several lines of action to promote cancer research in France. First, it organizes calls for proposals, and their evaluation in three main research areas: basic cancer biology, clinical and translational research, and human, social and economic sciences and funds selected projects. Second, INCa vigorously supports the development of biological resources and their integration into a coherent national and European network. Third, it initiates and manages large clinical trials such as the PHARE trial. Finally, INCa develops large databases relevant to cancer. For each of these different lines of action INCa has developed specific teams within its organization.

Key Staff

  • Professor Gilles Thomas

Contact details

THe Institut National du Cancer
52, avenue André Morizet
92513 Boulogne Billancourt Cedex

Stichting Het Nederlands Kanker Instituut

Stichting Het Nederlands Kanker Instituut

The Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands, founded in 1914, is the only Dutch Cancer Centre combining hospital and research laboratories in a single independent organisation. The annual budget for the NKI is approximately 38 million euros. The institute has a strong translational research programme. The main focus of the Department of Pathology is molecular profiling of tumors for hereditary susceptibility, prognosis and therapy response and analysis of DNA damage repair germline mutations to assess the risks of radiation-induced breast cancer. DNA expression microarray and copy number SNP array analyses in combination with detailed clinical annotation form the major technical activities underpinning these programs.

Key Staff

  • Dr Laura van't Veer
  • Dr Annegien Broeks
  • Dr Ron M. Kerkhoven
  • Mr Jelle Wesseling

Contact details

The Netherlands Cancer Institute
Plesmanlaan 121
1066 CX Amsterdam
The Netherlands

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