Neoplasms

Symptoms and General Pathology

All Conditions

Neoplasm Metastasis

Neoplastic Processes

Subjects will have their cancers biopsied and blood samples taken; both will undergo genomic sequencing and analysis

Genome sequencing

Janessa J Laskin, MD

Marco Marra, PhD

Janessa J Laskin, MD, FRCPC

The genomic heterogeneity of cancers implies that to effectively use targeted therapies the investigators will need to assess each individual cancer and match it to a biologically relevant targeted therapy. The investigators will use full genome sequencing to try to identify cancer "drivers" and corresponding drugs that may inhibit these pathways.

Carcinogenesis is an immensely complex process such that even within a histologic cancer subtype - for example adenocarcinoma of the lung or breast - there is significant variability in cancer behaviour and response to therapy. Analyses of individual patients demonstrate unique molecular signatures for every cancer examined. Frequently, multiple different pathways are involved in disease growth and progression and the dominant process varies from person to person and perhaps even within different sites of disease within one person. As well these variations evolve in response to treatment.

Recognizing genetic aberrations that promote disease facilitates targeted treatment; this has been demonstrated in several small subgroups of cancers in which specific genetic mutations or translocations have been successfully treated with targeted chemotherapy agents. With many recognized mutations and aberrations, personalized evaluation of the genetic signature encoded in DNA and RNA may provide important diagnostic information and potentially enable directed therapy to the appropriate oncologic pathway thereby providing information to help guide chemotherapy choices

Our initial pilot project demonstrated the feasibility of this approach at our institution (with 100 patients). We now know it is possible to identify and consent patients, sequence the genome and transcriptome, analyze and report abnormalities, and identify potential actionable targets in a clinically relevant time frame.

The Personalized OncoGenomics (POG) program has been operational across the province of BC since 2012. The initial two-year phase established the infrastructure and workflow by which patients with metastatic or incurable cancers could be identified, consented, and biopsied for genomic sequencing in a clinically accredited lab (Laskin et al., 2015). The next phase of the POG program (2014 - 2017) included a strong educational and engagement process such that 83 (80%) of the medical oncologists at BC Cancer were trained to consent and enroll patients onto POG. This means that the oncology community in BC has a broad education in cancer genomics and how these data may be applied to individual patients. Since 2017, the program has been integrated into the Vancouver Cancer Centre's phase 1 clinical trials unit and the focus has shifted to use the study patients and data to address more focused clinical therapeutic trials such as the CCTG CAPTUR study (Skamene et al., 2018). POG-like WGTA has been the driving force behind the creation of the Terry Fox Marathon of Hope Cancer Centre Network (MOHCCN) which is a national program for cancer genomic data sharing across Canada.

The overarching theme of this POG Program is to create a comprehensive cataloguing of somatic cancer mutations and cellular pathway abnormalities that could generate profound insights into genetic patterns that underlie particular cancer phenotypes, and provide valuable prognostic and predictive information.

Eligible subjects will have several samples analyzed: a fresh tumour biopsy (typically 5 cores are required), a blood sample for normal comparison and archival tumours when available. Also, technology has improved such that we may consider using paraffin embedded materials. Comprehensive DNA and RNA sequencing is performed followed by an in-depth bioinformatic analysis to identify somatic mutations, gene expression changes or other abnormalities that might be cancer "drivers" or provide actionable (diagnostic) or druggable targets. The POG team meets every week to discuss the detailed genomic reports for patients, consider additional validation tests when necessary, and debate research questions. The clinicians (typically 5 - 10) come to a consensus on what systemic therapies might be appropriate based on these results. Whenever possible subjects are matched to clinical trials.

Personalized Oncogenomics (POG) Program of British Columbia

Personalized OncoGenomics (POG) Program of British Columbia: Connecting Cancer Genomics to Cancer Care

This outcome will allow us to study how often in-depth genomic data impacts on clinical decision-making in a general oncology population. It will help describe how useful or important this sort of data is in daily practice.

Accumulation of genomic information linked to treatment/outcome data will greatly enhance our knowledge and understanding of cancers and response to treatment.

BC Cancer Foundation

British Columbia Cancer Agency

Patients enrolled in POG who initiated WGTA between July 2014 and December 2017

Matched controls who received usual care and were diagnosed with metastatic cancer prior to December 2017

POG-related WGTA generally involves collecting biopsy samples, applying whole-genome and transcriptome sequencing, and using bioinformatics analysis to interpret sequence data and inform clinical decision-making.

Initiation of POG-related WGTA

Usual care, not involving the initiation of POG-related WGTA

Usual care

This study aims to determine the clinical effectiveness of whole-genome and transcriptome analysis (WGTA) to guide advanced cancer care. The study setting is the British Columbia (BC) Personalized OncoGenomics (POG) program, a single group research study of WGTA guiding treatment planning for patients with advanced, incurable cancers (NCT02155621). To characterize clinical effectiveness, the survival impacts of POG's approach compared to usual care in matched controls will be estimated.

WGTA provides an opportunity to improve health outcomes for patients by tailoring treatments to each individual's genomic profile. The BC POG Program is a single arm research study integrating WGTA information into clinical decision-making for patients with advanced stage, incurable cancers.The clinical effectiveness of POG's approach is unknown. This retrospective quasi-experimental observational study will estimate the real-world effectiveness of WGTA for guiding advanced cancer care. To identify a counterfactual for POG's single-arm approach, matching methods combined with administrative healthcare data will be used. The survival impacts of POG's approach compared to usual care in matched controls will then be estimated.

Specific Aims and Hypotheses

This study aims to estimate the overall survival effects of POG's approach versus usual care for patients with advanced cancers.

Hypothesis (null): there is no difference in survival across POG and usual care patients

Hypothesis (alternative): POG patients who initiated WGTA live longer, on average, than usual care patients

Study Design

This study will apply a retrospective cohort design. Cohorts will include patients who consented to POG and underwent a biopsy for WGTA between July 2014 and December 2017 and matched usual care controls. POG patients who enrolled prior to July 2014 will be excluded from our study because during this feasibility period, referring clinicians employed a high level of case-by-case recruitment selection. Usual care patients will be matched to POG patients using supervised learning techniques. The study period will range from patient's time of metastatic cancer diagnosis to December 31 2018.

Data Sources

De-identified linked population-based administrative datasets will be obtained from BC Cancer for all adult patients (\>18 years) diagnosed with cancers in BC prior to December 2017. POG patients will be identified from the BC Cancer Outcomes and Surveillance Integration System (OaSIS) POG Module Database. Eligible control patients will be identified from the BC Cancer Registry, a population-based provincial cancer registry. These data will be linked with data from the BC Cancer Pharmacy Database, Radiotherapy Database, and Cancer Agency Information System (CAIS) using agency-specific identifiers.

Statistical Approach

The investigators will match POG patients and usual care patients based on their date of metastatic disease diagnosis. They will apply 1:1 genetic algorithm-based matching (1:2 in sensitivity analysis) and match patients on propensity scores and baseline covariates, including patient demographics, clinical characteristics, treatment histories, and healthcare utilization prior to metastatic disease diagnosis. When necessary, matching analyses will be stratified to account for variation across cancer types.

To estimate overall survival in POG patients and matched controls, non-parametric and parametric survival analyses will be used. These analyses will be adjusted for censoring. The investigators will explore heterogeneity in clinical effectiveness across cancer subtypes through subgroup analysis and use scenario analysis to determine the impact of future changes in the application of WGTA on clinical effectiveness.

Real-world Clinical Effectiveness of Whole Genome and Transcriptome Analysis to Guide Advanced Cancer Care

Retrospective Observational Study Determining the Clinical Effectiveness of Whole Genome and Transcriptome Analysis to Guide Advanced Cancer Care

The patient-level administrative data used in this retrospective study are confidential and will not be made available in a public repository, in accordance with institutional policies.

Study title	NCT ID	Conditions	Interventions	Eligibility	Organization
Personalized Oncogenomics (POG) Program of British Columbia	NCT02155621	Metastatic Canc... Advanced Cancer... Cancers That Ca...	Genome sequenci...	18 Years - 85 Years	British Columbia Cancer Agency
Real-world Clinical Effectiveness of Whole Genome and Transcriptome Analysis to Guide Advanced Cancer Care	NCT04141397	Metastatic Canc... Advanced Cancer Cancers That Ca...	Initiation of P... Usual care	19 Years - 85 Years	British Columbia Cancer Agency
Real-world Clinical Effectiveness of Whole Genome and Transcriptome Analysis to Guide Advanced Cancer Care	NCT04141397	Metastatic Canc... Advanced Cancer Cancers That Ca...	Initiation of P... Usual care	19 Years - 85 Years	British Columbia Cancer Agency

Spots Global Cancer Trial Database for cancers that cannot be treated with curative intent