Jacqueline Staring, Programme Manager at Oncode Institute, heads up the Infrastructure & Technologies Programme, the Drug Repurposing Programme, and the soon to be launched Technology Access Programme. She discusses the facilities and technologies that are available for the Oncode research community and how they will support and accelerate oncology research.

Jacqueline: "Many institutes have technologies and facilities available that provide for the basic needs of their own researchers. Since one of the main goals of Oncode is to support the sharing of knowledge, expertise, and equipment within our network of researchers, we came up with several ideas on how to expand on technological support for our researchers. First, we wanted to make sure that some of the more successful and already existing facilities and technologies would become available for all researchers. Secondly, Oncode planned to invest in new facilities and technologies that were not available yet for our research community and would complement the existing infrastructure of our partner institutes.”

It all kicked off with the Technologies and Infrastructure Programme. Via several calls, Oncode Investigators were invited to propose investments in certain technologies that were going to be useful for the whole community. Many different ideas were funded and a full overview of the list of technologies can be found here (scroll down).

Jacqueline: "Once most of the technologies from those calls were installed, we also wanted to give a push to facilities, to make sure they would be available to the Oncode community. An example is the Proteins4Oncode facility at the NKI, headed up by Anastassis (Tassos) Perrakis and Patrick Celie. This Protein Facility has years of experience in supporting NKI researches and will now extent its support to the entire Oncode community with expressing and purifying proteins, help with characterisation, production and purification of antibodies for research purposes, and crystallisation efforts. An example of a completely new facility is the Oncode Single-cell (epi) genome sequencing facility at the Hubrecht Institute, headed up by Alexander van Oudenaarden and managed by Floris van den Brekel. This facility will support Oncode researchers with DNA at the level of individual cells. They offer regular genomic DNA sequencing of single cells but specialize in analysing epigenetic markers in single cells. The unique aspect of this programme is not only that it is creating the availability of specific equipment for researchers to use, but that it offers the expertise needed for the optimal use of these often very specialized tools. This means experienced researchers will be ready to help and support you with your research requests.”

And it’s not just the facilities that will add value, Oncode also looks into the future by investing in specific computational infrastructure supporting large patient material databases and specific servers that can accommodate data analysis that requires machine learning applications.

Jacqueline: “Researchers’ needs with regards to data analysis are getting more and more complex. That’s why we focus on investing in computing infrastructure to support machine learning. An example is the Oncode GPU infrastructure which enables Artificial Intelligence and Deep Learning applications at the NKI, the UMCU and the UMCG, and is coordinated by Anastassis (Tassos) Perrakis. Oncode also invested in a platform for clinical colorectal cancer samples, which is headed by Louis Vermeulen at the Amsterdam UMC and managed by Geraldine Vink. This online platform contains data of all available materials (tissue, blood, residual material) from clinical colorectal cancer studies that can be used for research purposes. The development of this platform will be completed together with the Prospective National CRC cohort (PLCRC) and will be accessible for all Oncode researchers.”

Researchers that want to have a full overview of the availabilities with regards to technologies, facilities, infrastructures, and online platforms are encouraged to login at the Oncode Community Platform*, where all information is available. Or they can contact Jacqueline directly.

Jacqueline: “I would like to stress that a lot is possible within the Oncode Institute and would really like to encourage all Oncode researchers to make use of the opportunities. You have access to technologies that might not have been available to you previously. At Oncode we will keep focusing on expanding this in the future. Therefore, all Oncode researchers that have a good idea that could benefit the whole research community can contact me to discuss it. I’m very interested to hear what kind of technologies or facilities they think are crucial for our cancer research community.”

*All Oncode researchers have access to the Oncode Community Platform, if you have troubles logging in, please contact [email protected] and don’t hesitate to update your own personal community platform page.