Our ovarian cancer team continues to build infrastructure for innovative pilot study and biobank.
October 7, 2020
The Ovarian team has used these past months to hone and polish the infrastructure for the High Grade Serous Ovarian Cancer Initiative and to ensure that high quality molecular data can be generated from the samples. This includes both the pilot project that focuses on changes in the micro-environment, and the retrospective study that looks back at tissue.
Focus of the project
Our focus is to define the role of the fallopian tube micro-environment in the development of high grade serous ovarian cancer (fallopian tube being the most common ovarian cancer), with the ultimate objective to find targets for prevention and markers of early disease onset for early detection.
In order to develop a robust and innovative research plan, we invited a multidisciplinary team of roughly 25 world class ovarian cancer researchers from across the US and Canada to an initial two day planning meeting in March 2019 in Los Gatos, California. The meeting was highly successful. The number of promising ideas exceeded our available funding level. Over the ensuing months the Executive Committee worked to refine and finalize our research proposal and also put in place the necessary infrastructure to conduct our studies.
What problem is the team trying to solve? Our overall plan includes a series of innovate pilot studies specifically designed to demonstrate the power of our team and generate preliminary data that can be leveraged to compete for large grants by the end of a two year period. The research will be performed in two phases: first, a retrospective phase that involves analysis of previously collected, banked fallopian tube samples with associated clinical information, and second, a prospective study, that includes newly collected samples, each with the goal of identifying what changes in the molecular landscape signal cancer.
Our progress March – Summer 2020. During these past months, the team has finalized the infrastructure for the pilot program and has worked to ensure that the expected high quality molecular data from our samples can be achieved. The process for sample sharing has been completed. Additionally, reviews, discussions, and decisions have been held to work out a draft of the high-quality protocol necessary for all team members to follow. 6 potential sites have been identified. We are testing our data management processes. This includes a portal for sharing and annotating data among multiple investigators and analysts. Canary Foundation has experience in this field.
Next steps: the in-person clinical aspect of the pilot will resume when each of the participating sites are reopened. When further steps in reopening allow, clinical sites will be responsible for providing patient samples and annotated clinical and pathologic data in a timely and cost-effective way. Each site includes a collaborative PI who has a robust system in place for conducting translational research studies, banking samples and linking clinical information.
Additionally, steps are being taken to identify and put in place a central project manager. An interim plan is in place utilizing resources at the University of Pennsylvania.
Clinical data and sample coordination center: The University of Pennsylvania leader is Michael Feldman. We are working with the team at UPenn to write sample protocols and requirements and to finalize the overall collaboration agreement that will be signed by all institutions. The coordinating center will receive samples from clinical sites, perform quality control, and prepare and ship samples to molecular profiling sites. The center will also maintain the clinical database of participants linked to their sample information. The clinical data will be linked later to the molecular data for each of the samples and participants.
Clinical teams: when further steps in reopening allow, clinical sites will be responsible for providing patient samples and annotated clinical and pathologic data in a timely and cost-effective way.
Molecular profiling sites: Molecular analyses will include bulk RNA and DNA sequencing, global methylome profiling, proteomics with spatial profiling, single cell analyses using the Nanostring DSP platforms.
Data management and analysis center: We have multiple types of data that need to be securely stored and annotated. We are using a similar structure to that used by the large NIH-funded effort, TCGA. Raw data will be hosted in the data center managed by Adam Olshen at UCSF. We will run data analysis pipelines and upload processed data into a program that will function as a portal for sharing and annotating data among multiple investigators and analysts. Canary Foundation has experience in this field.
Shaping bioinformatics. Our leadership and analysis team leaders are enthusiastic about working together using Synapse and the Sage engineers. The associated infrastructure and analysis plan from our bioinformaticians Adam Olshen (UCSF) and
Hui Shen (Van Andel) has been reviewed and approved by the group.
Checking our system.
- Testing of infrastructure and logistics with a small set of samples will include:
- Assessing technical issues
- Management of resources
- Rapid course correction procedures
- Generating first data set
- Send samples through the pipeline (10 BRCA mutation carriers)
- Check quality control measures on data set
Working as a team. Part of the strategy is to demonstrate our ability to work together and generate data so that we are able to apply for additional support from external agencies (e.g. government or foundations). The team is actively making connections to seek out the best funding opportunities as part of our future plan, and the breadth of expertise in the team and their ability to work well together go a long way in securing future funding.