How state-of-the-art bioinformatics software is personalising patient care

21 March 2018
Key Researchers
Researchers at the Walter and Eliza Hall Institute have developed an innovative bioinformatics software tool that is the new state-of-the-art in cancer genome analysis.

The GRIDSS (Genome Rearrangement IDentification Software Suite) software is being used to unravel complex tumour mutations to personalise cancer treatment. The technology is already being used to improve the care of cancer patients in Victoria.

At a glance

  • Chromosome rearrangements can cause cancer or drive the evolution and spread of cancer.
  • Institute researchers have created a state-of-the-art way of quickly and accurately detecting chromosome rearrangements in patient’s cancers.
  • The technology is already being used as part of cancer patient care in Victoria.

Chromosome rearrangements and cancer

Two researchers drawing on whiteboard
Dr Daniel Cameron (left) and Professor Tony Papenfuss
have developed innovative bioinformatics software to
unravel complex tumour mutations.

Cancer is a catch-all term for a wide range of diseases caused by the uncontrolled growth and spread of cells that are abnormal because of changes in their DNA.

In some cancers, the cell undergoes significant changes that see whole chunks of DNA moved from one place on the chromosome to another. Chromosome rearrangements usually occur due to a chromosome ‘break’ that is incorrectly ‘repaired’ by in-built DNA repair mechanisms in the cell. They are important because they can cause cancers, or drive the evolution or spread of cancers.

Detecting chromosomal rearrangements in cancers is essential for researchers to understand more about how cancers grow and evolve. However identifying gene rearrangements in cancer can be particularly difficult.

Professor Tony Papenfuss, Dr Daniel Cameron and other members of the team at the Walter and Eliza Hall Institute developed a software program that is the best in the world at detecting chromosomal catastrophes. The method was published in the journal Genome Research.

State-of-the-art tool to unravel cancer

Professor Papenfuss said the GRIDSS program outperformed current tools available for doing this kind of cancer research.

“It’s really the new state-of-the-art technology, using a selection of novel algorithms that have been specially designed to identify chromosomal rearrangements in cancer,” Professor Papenfuss said.

“There are several very good tools available but also many that are not fit for purpose—too slow, crash, miss rearrangements, or make too many mistakes.”

He said the GRIDSS software tool, developed during Dr Cameron’s PhD, built on the ideas of other programs but added several innovative new ideas that dramatically improved results.

“Producing high specificity and sensitivity data is really important, and that’s what we have done. It can be applied to a broad range of experimental designs to quickly and reliably identify the chromosomal rearrangements driving cancer.”

Professor Papenfuss said his team’s expertise and experience in unravelling the blueprint of cancer was essential for this new technology.

“We’ve been working in this space for a while and have learned what biology to incorporate into our computational methods as well as how to help specialists understand how to interpret and apply the findings,” he said.

Helping cancer patients with bioinformatics

For cancer specialists, understanding cancer at a molecular level is vital for their patients to receive the best treatment for their particular cancer, to test whether a treatment is working, and to keep track of any changes in the cancer.

The new bioinformatics tool is already being used at Victoria’s Peter MacCallum Cancer Centre to identify genetic mutations in cancer and better target treatments to the particular patient’s cancer.

“Through the Peter Mac, we are already seeing patient’s benefiting from this new technology.

“Some types of cancers, such as sarcomas and some leukaemias, are particularly associated with chromosome rearrangements. Understanding the molecular basis of a patient’s cancer helps to inform how specialists treat the cancer, and identify novel targets for creating new anti-cancer drugs,” Professor Papenfuss said.

“Biomedical research has become inherently multidisciplinary – now we have ‘wet’ and ‘dry’ lab scientists working together to answer big biological questions and develop new tools so other people can benefit from our research,” he said.

The research was supported by the Australian National Health and Medical Research Council and the Victorian Government.

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