Computational Biology Software

The computational biology team develop analytical software with broad distribution through open source repositories.

Our research group develops computational methods for the analysis of high throughput cancer genomics data.  We use machine learning techniques to develop statistical models to infer genomic abnormalities from next generation sequencing data and high-density genotyping arrays.  Dr. Andrew Roth and Dr. Sohrab Shah work with Dr. David Huntsman and Dr. Sam Aparicio who lead ovarian cancer and breast cancer research respectively at BC Cancer, part of the Provincial Health Services Authority. We focus on the analysis of clinical samples with the goal of detecting genetic abnormalities in tumour genome that might be developed into diagnostics, prognostics or novel therapeutic targets.  Most of our software is released under an open source license and is free to download here.

Precision Medicine for Breast Cancer Research (B-PRECISE) Biorepository

The  Department of Molecular Oncology hosts the Precision Medicine for Breast Cancer Research (B-PRECISE) biorepository. 

A biobank collects, stores and gives out to other researchers human samples (for example, tissue, saliva, blood, fluids, stem cells, blood etc) health records treatment and diagnostic data connected to these samples. Our primary biobanking protocol,B-PRECISE, Tumor Tissue Repository (B-PRECISE, TTR) primary goal is to collect biological specimens  including residual tumor tissues through best practices. Through this, our researchers will develop new tools that could be used for precision medicine to help patients in the future. As of 2019, our biorepository at the BC Cancer Research Centre in Vancouver holds approximately 8000 breast cancer specimens. 

Our Research platform has developed Mission, Vision and Objective statements and defined 4 areas of investigation.

B-PRECISE is committed to reducing the burden of breast cancer by identifying the causes and treatment interventions for individuals.

The B-PRECISE biorepository will support  research studies by facilitating access to a unique population- based resource that will enable translational research and ultimately result in improved treatment and intervention for individuals with breast cancer. 

To build a research resource which includes  tissue, blood and data (including sequencing data, imaging, treatment, monitoring, and outcomes data ) from a cohort of newly diagnosed breast cancer patients from across  British Columbia (BC) 
Our biorepository is comprised of specimens from participants all over BC as well as collaborative  cases/data that came from the UK. The Canada-UK project named METABRIC aimed to classify breast tumors into further subcategories, based on molecular signatures to help determine the optimal course of treatment. You can read more on the METABRIC study here:

Currently, our B-PRECISE research program has four primary areas of investigation:
1. Studying single cells to fully understand the biology of breast cancer and identify new  subtypes, including “omics” analysis.
2. Identifying patterns associated with disease response with an aim to develop new diagnostic tools
3. Assessing the effectiveness of standard of care treatments
4. Supporting collaborative research with investigators in breast cancer and cancer mechanisms
in general outside of the B-precise program. 

If you have questions about our B-PRECISE  Biorepository please contact:

Principal Investigator and Director 
Dr. Samuel Aparicio
Leader, Provincial Breast Cancer Clinical Research Program 
Cherie Bates

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