Ontario-wide Cancer TArgeted Nucleic Acid Evaluation

A recent survey of clinical genetic testing laboratories for cancer diagnostics by the Molecular Oncology Advisory Committee for Cancer Care Ontario identified disparities in access and use patterns for next generation sequencing (NGS) across the province of Ontario. All fourteen responding laboratories indicated that NGS instruments were either currently being used for clinical testing, were in the validation stage, or that they were planning to purchase NGS instruments within the near future. Respondents were uncertain about what tests should be performed, how costing and reimbursement would be addressed by the provincial funding agency (e.g. individual tests vs. panels), and how to deal with informatics issues from NGS testing, such as storage, variant interpretation, and utilization over the long term.

Given the increasing use of multi-gene somatic mutation testing in routine clinical cancer care (e.g. KRAS, NRAS, BRAF mutations in colorectal cancer, EGFR mutation and ALK translocation in non-small cell lung cancer, and BRAF, NRAS, and cKIT mutations in malignant melanoma), there is a need to expand the infrastructure for NGS panel testing in clinical laboratories. With a single payer provincial health care system, there is also an opportunity to develop a provincial-wide registry of NGS panel-based testing results and repository of genomically-characterized and clinically-annotated tumor tissues and blood samples to accelerate the development of additional "omic"-based tests for clinical use.

This study will enroll patients with advanced, incurable solid tumors at selected Ontario hospitals receiving standard palliative treatment(s). Archival formalin-fixed paraffin embedded (FFPE) tumor tissue will be requested and undergo targeted panel sequencing. An additional FFPE tissue sample will be requested at the same time for future research purposes. Patients will also be asked to provide blood samples for future research. A selected number of genes will be annotated in a research report provided to their treating oncologist. In addition to the clinically reported variants, targeted NGS testing results for all tested genes will be captured in a clinical research database that can be accessed by the treating oncologist in a secure web-based portal.

Following the reporting of targeted DNA sequencing results into the web-portal, remaining tumor DNA will be stored in the clinical testing laboratories. Blood samples collected at the time of consent and additional FFPE research blocks or slides collected for research will be transferred to a centralized biorepository maintained by the Ontario Tumour Bank (OTB) for more comprehensive analysis at the Princess Margaret (PM)-Ontario Institute for Cancer Research (OICR) Translational Genomics Laboratory (TGL). Blood will undergo standard germline DNA extraction and plasma processing for future circulating tumor DNA (ctDNA) and RNA (ctRNA) isolation at the PM-OICR TGL. Selected patient samples will be further characterized at the PM-OICR TGL for test development, additional sequencing, or discovery research.

All patients will be asked to provide permission for data-sharing with other cancer researchers. The consent will also include a provision for review of patient health records through review of patient charts or administrative databases (i.e. Cancer Care Ontario New Drug Funding Program, Provincial Cancer Registry, etc.) to obtain addition information about time on drug treatments and survival.