What are the plans of your task force for the coming years?
In the currently ongoing iProfiler (Module 1); patients are being tested using the Foundation One assay from Roche as well as the large, solid-tumour gene panel established within the CCE. The CCE panel analysis is performed as a centralised, collaborative effort, where data generation (library preparation from FFPE and matched germline patient samples followed by sequencing) is done at Cancer Molecular Diagnostics Laboratory, Cambridge; Bioinformatic analysis is performed at NKI, Amsterdam, and final variant annotation prior to clinical interpretation is carried out at KI, Stockholm, utilising the MTB Portal.
Within the task force, we are currently working on transitioning to a decentralised testing so that all centres will eventually carry out the molecular profiling of their patients at their own facility. Key points we are currently addressing include defining the minimum panel content which all centres need to provide, as well as establishing the quality assurance program which will allow us to demonstrate consistency and robustness of the assays across the entire CCE network. During the transition period, whilst the individual centres are establishing their assay capabilities, samples can still be sent to one of the other centres for profiling. This will ensure a smooth transition from the current centralised testing regime to the decentralised one.
A future CCE gene panel minimum content will be defined based on the needs of the clinical trials task force and collaborating pharma partners.
In parallel, the task force is working on establishing quality assured assays for the detection of copy-number aberrations using RNA sequencing to address and anticipate future profiling requirements. The GTF will continue to support clinical trials by establishing additional genomic assays whenever needed, using the expertise from each
At many centers broad gene panel-based testing is either entering into the routine pathology diagnostic setting, or starting to be used at scale in parallel with routine molecular pathology testing. The transition to a decentralised testing regime ultimately promises that a significantly higher number of patients can be analysed across the network of centers. We also anticipate that the turnaround time of the molecular analysis will be shortened, enabling the faster recruitment of patients into clinical trials.
The diversification of the assay portfolio through the inclusion of RNAseq based detection of copy number aberrations will allow the expansion of the portfolio of clinical trials.
The GTF continues to liaise with the virtual data center to ensure that the generated data and its associated metadata is presented in a harmonised way, using existing and emerging international standards to facilitate the integration of data across the different centers.