Research at the CPCT has shown that metastases are genetically very different, both at the nucleotide and chromosomal level (Vermaat et al, 2011, click here; Kloosterman et al, 2011, click here). Determining the optimal treatment strategy based on mutation profiles must therefore be realized on the tissue that requires treatment instead of on material stored at an earlier stage of treatment. In other words, the treatment of metastasized cancer should be focused on specific properties of the metastasis. As this is not the standard in cancer diagnostics, the CPCT has developed protocols for clinical trials in which a biopsy of the metastasis and blood material of patients with metastasized cancer are obtained in an efficient way.
The CPCT Next-Generation Sequencing Core Facility
All DNA samples from the CPCT clinical trials are processed in its ‘Next Generation Sequencing Core Facility’, located in the facilities of the Hartwig Medical Foundation (Amsterdam Science Park, www.hartwigmedicalfoundation.nl). By using the latest sequencing equipment, this facility has developed standardized methods and quality control to generate mutation profiles for large numbers of samples.
This is realized by means of Whole Genome Sequencing, with which we can map DNA mutations in the complete DNA material. Via bioinformatics tools we then compose a mutation profile per patient, which may be indicative for assigning a patient to a specific clinical trial. By means of systems biology methods we identify predictive biomarkers based on mutation profiles and the clinical data that become available during the clinical trials. NGS technology is therefore of major importance to unravelling the development of cancer and developing new treatment strategies.
The Nederlands Tijdschrift voor Oncologie (Dutch Journal of Oncology) published a review article in December 2011 about the CPCT and our application of DNA sequencing for personalized cancer treatment. Download the article here.