Abstract

Analysis Challenges and Solutions for Cancer Genomics Data

Anthony Papenfuss, Head, Bioinformatics and Cancer Genomics Laboratory, Peter MacCallum Cancer Centre

In the research and clinical settings, cancer genomics is now generating huge quantities of next generation sequencing data. Over the last 7 or so years, enormous progress has been made in analysis methods, but many challenges remain and new challenges continue to emerge. These are thrown up by new technology platforms (such as custom capture panels), new data, and new research and clinical applications. 

In this talk, I will discuss some of the challenges we have faced, our solutions, and the open questions. I will cover analysis in clinical cancer genomics and genomics discovery projects. Clinical cancer genomics demands more of an engineering focus to analysis than research. We have made some progress in developing tools to support robust, clinically defensible analyses, including for analysis, method validation and reporting. Research also benefits from robust, validated pipelines, but frequently requires boutique methods and a higher level of creativity.

I will cover single nucleotide variants and copy number