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Video: A Bioinformatics Pipeline for Analyzing Patient Tumours

In this video from WestGrid in Canada, Dr. Yussanne Ma from the Michael Smith Genome Sciences Centre describes how 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.

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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