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Advanced Research Computing and Genomics: A bioinformatics pipeline for analyzing whole genome and transcriptome sequence data from individual patient tumours

Genome Sciences Centre

Date:

Speaker Info:

Dr. Yussanne Ma
Group Leader, Bioinformatics
Genome Sciences Centre

Description

In this session, WestGrid will host a guest speaker from the Michael Smith Genome Sciences Centre, one of fifteen research programs that operate as part of the BC Cancer Research Centre. The world-class scientific team at the Genome Sciences Centre has played a major role in advancing the fields of genomics and bioinformatics. In July 2014, the Genome Sciences Centre announced a partnership with WestGrid and Compute Canada to join Compute Canada's national platform of computing sites, benefiting researchers across Canada with increased access to bioinformatics software, expertise and extremely secure computing storage. 

Speaker:

Dr. Yussanne Ma
Group Leader, Bioinformatics
Genome Sciences Centre

Abstract:

Dr. Yussanne Ma leads the bioinformatics group at Canada's Michael Smith Genome Sciences Centre in Vancouver, BC. In this session, she will discuss the ways high performance computing supports her research group's work, highlighting a recent project where a bioinformatics pipeline was built for the personalized onco-genomics project (POG) at the BC Cancer Agency. POG aims to use paired tumour/normal whole genome and transcriptome sequence information from an individual to comprehensively characterize a patient's tumour and inform treatment options within a clinically relevant timeframe. The bioinformatics pipeline developed for this project identifies the somatic abnormalities in a tumour, including single nucleotide variants (SNVs), indels, copy number variation (CNV), loss of heterozygosity (LOH), fusions, and gene expression. Interpretation of the somatic profiles are aided by a hand-curated knowledge base of targetable mutations, resistance and sensitivity markers which was developed in house. To date, 171 patients have been enrolled in the POG project, with over 50 cancer subtypes. So far, 120 patients have analysis completed, 14 are in process of being sequenced or analyzed, and 8 are pending biopsy.

In addition to this project, Yussanne's group is also collaborating with IBM on an implementation of its Watson Genomic Analytics platform, a novel IBM Watson solution for interpreting whole genome and transcriptome data from cancer samples to inform treatment. Yussanne's group is involved in the development of the solution and comparing the output to that of their pipeline developed for the POG project.

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