WORKPACKAGE 1

Retrospective DCIS data and tissue block collection

Hypothesis

Formalin fixed paraffin embedded (FFPE) tissue blocks can be curated with matched clinical data and from these adequate amounts of nucleic acids (DNA, RNA) can be extracted, whole sections provided for research and tissue microrarrays (TMAs) constructed from sections for WP 2,3 and 4. This WP comprises the curation of three large complementary cohorts:

 

retrospective (Dutch and US) or prospective (NHS Breast Screening Programme Sloane Project, UK) cohorts of DCIS with matched and annotated clinical and pathology data from which, through careful long-term follow-up, subsets of indolent versus aggressive DCIS have been identified for evaluation.

Workpackage 1 is responsible for the project objective to deliver DNA, RNA and sections from DCIS, normal tissues and recurrences of suitable quality and quantity to support WP2-WP4

Milestones

1.1 Deliver DNA/RNA for nucleic acid studies
1.2 Identify and accrue additional sample sets
1.3 Update clinical outcomes data to detect additional events and potential samples

WP1 is supported by The data management working group

Working group data management

In the DCIS project a diversity of clinical, imaging, biobank and experimental molecular biology data will be obtained and in prospective studies additional biosamples and data will be collected. For sustainable data management of these different types of data we will base our data management platform on the tools and expertise built up within the TraIT (Translational Research IT) consortium. IT infrastructure has to enable cross-cohort data retrieval and biomarker evaluation from the collection and harmonisation of very diverse clinical and molecular biology data. The data-integration platform ‘tranSMART’ will serve this central role, whereby the final or processed research data will become available for visualisation, data-integration and querying of information.

Good organisation of the data aggregation, data retrieval and sample ordering is imperative. For this, we will utilise the biobank catalogue procedures as operational within BBMRI-NL. The resulting data set as collected in tranSMART will be made available to the DCIS project community for hypothesis-free browsing of the available data in a user-friendly manner, as a first level analysis environment for biomarker selection. Finally, importing the ‘final’ or ‘processed’ data to cBioportal as well as tranSMART offers the DCIS community the opportunity to view the obtained data from different perspectives. The tranSMART and cBioportal communities are working together to enable easy transfer of data from tranSMART to cBioportal.

WP lead

Professor Alastair M. Thompson

Professor of Surgery

University of Texas, MD Anderson Cancer Center, Houston, TX, USA

Collaborator

Dr Elinor Sawyer

Clinical Oncologist

King’s College, London, UK