This week we profile a recent publication in Nature Communications from the lab of
Dr. Steven Jones (pictured, center) at Canada’s Michael Smith Genome Sciences Centre.
Can you provide a brief overview of your lab’s current research focus?
Our team uses bioinformatics to investigate the landscape of mutations present in cancer genomes and the early genomic events that give rise to and promote the progression of cancer. To achieve these goals, the lab analyzes Next Generation Sequencing data and develops novel computational approaches and methodologies. A significant aim of the research program is to find innovative ways to exploit specific genomic profiles within an individual cancer for therapeutic purposes. For example, we’ve identified a number of epigenetic modifications that may potentially be targeted to reverse the effects of cancer initiating mutations. Using computational approaches, such as molecular docking and molecular dynamics, we aim to identify and refine compounds that can modify the cancer epigenome.
What is the significance of the findings in this publication?
The Platform for Oncogenomic Reporting and Interpretation (PORI, https://bcgsc.github.io/pori) described in our recent Nature Communications publication integrates multiple knowledge bases and ontologies into one platform for the purposes of sharing relevant data from genome analysis related to precision oncology. PORI is composed of the graph-based knowledge base, GraphKB, and reporting software, Integrated Pipeline Reports (IPR). It is the first open-source, production-ready and scalable software platform designed to communicate clinically relevant oncogenomic information. PORI accommodates variant, gene expression and complex molecular data and reports clinically relevant knowledge curated from multiple external knowledge resources into a genomic report that can be disseminated to clinical and research experts.
What are the next steps for this research?
Although PORI represents an important first step in creating an open-source standard tool for reporting in precision oncology, there are still many avenues for future development. Currently, the platform focuses on creating research reports and future iterations could include clinically accreditable formats of the report. In addition, the application of data captured from user actions during the analysis process will be used to improve and further automating future analysis. As more knowledge is curated, each patient will match more annotations and reports will become increasingly verbose. Facilitating the complex analysis associated with precision oncology in cancer will not only have direct benefit to the patients analyzed but also the process as a whole through improved communication and transparency.
If you’d like to mention your funding sources, please list them.
This work would not be possible without the participation of our patients and families, the Personalized OnocGenomics team, Canada’s Michael Smith Genome Sciences Centre platform, and the generous support of the BC Cancer Foundation and Genome British Columbia. We also acknowledge contributions towards equipment and infrastructure from Genome Canada and Genome BC, Canada Foundation for Innovation, the BC Knowledge Development Fund, and the Canada Research Chairs program.
