Genome Informatics

John Pearson


The Genome Informatics Group works on the analysis of next-generation sequencing (NGS) data and its research and clinical applications, particularly with respect to cancer. Cancer is increasingly being viewed as a disease where the tissue of origin is less important therapeutically than the unique spectrum of mutations found in the individual patient’s tumour.

NGS is the key technology used to catalogue mutations in both DNA and RNA and while it has been a research staple for over five years, it is only now starting to make inroads into the clinic. NGS is a high-throughput genomics technology with significant computational and storage requirements – the data for each tumour/normal sample pair can up to half a terabyte of disk to store and tens of thousands of CPU hours to analyse.

The absence of standardised cluster hardware and analysis workflows has been a key factor keeping NGS in a research setting and out of hospitals and pathology departments and the Bioinformatics group is working on methodologies to address that deficit.

The team originally came together as part of Australia’s International Cancer Genomics Consortium (ICGC) effort, sequencing and analysing over 500 samples from pancreatic and ovarian cancer patients. The Australian team has submitted more cancer sequencing data to ICGC than any other member nation apart from the USA.


  • somatic variant calling from tumour/normal DNA comparison including SNVs, small indels, structural variants and copy number changes
  • in silico validation of variants using RNA and other sequencing types
  • pathogen screening
  • telomere quantification

External Collaborators

  • Professor Sean Grimmond, Queensland Centre for Medical Genomics
  • Professor Andrew Biankin, Garvan Institute for Medical Research
  • Dr Nicola Waddell, Queensland Centre for Medical Genomics
  • Professor David Bowtell, Peter MacCallum Cancer Centre
  • Dr Pamela Pollock, Institute of Health Biomedical Innovation (IHBI), QUT