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Individualised cancer treatment one step closer following global study

Scientists are one step closer to being able to choose the best drugs to target individual cancer patients following a landmark global study involving researchers from QIMR Berghofer Medical Research Institute.

The study was conducted as part of the International Cancer Genomics Consortium (ICGC), and involved 83 researchers from 78 research institutes worldwide, including three scientists from QIMR Berghofer. The study was led by the Centro Nacional de Analisis Genómico (CNAG-CRG) in Spain and the German Cancer Research Center (DKFZ).

The findings have been published in the highly prestigious journal Nature Communications.

Cancer is caused by mutations in genes. These mutations can be targeted with drugs, but scientists have to correctly identify which mutations are present in any individual cancer to know which drugs are most likely to be effective in treating that cancer.

Research institutes across the world have designed and developed different software to identify which mutations are present in different cancers. However, while the software can identify mutations, it can also produce errors. To combat this, researchers at QIMR Berghofer have developed a second “layer” of software to detect the errors and confirm which cancer-causing mutations are present.

The aim of this study was to compare the effectiveness and quality of the different combinations of software (known as “pipelines”) that each of the different participating institutes used to find the genetic mutations that cause cancer.

The study found there were large differences in the methods the different research institutes used to find cancer-causing mutations and in the quality of the results. The study also found that these differences led to dramatic discrepancies in the number and types of gene mutations that the different institutes detected when they were working from the same data.

Co-author and head of QIMR Berghofer’s Genome Informatics Group John Pearson said the study clearly showed that not all mutation-hunting software was equally effective, and a focus on the second step of the process was critical for ensuring quality control.

“We were pleased to see that QIMR Berghofer’s software was identified as one of the top performers,” Mr Pearson said.

“We believe this was due to the combination of our mutation-hunting software with the second layer of customised, quality-control software.

“However, we cannot rest on our laurels. This technology is constantly advancing and QIMR Berghofer is continually testing and adapting its methods to ensure the Institute remains a world leader in this field.

“This will pave the way for better and faster methods for accurately identifying the mutations present in individual cancers.

“We hope this will eventually allow doctors to customise each patient’s treatment by prescribing the drugs that are most effective in treating the mutations that are present in a particular cancer.”

Dr Ann-Marie Patch from QIMR Berghofer’s Medical Genomics team said the study showed the importance of quality control in the process.

“Different institutes that used the same initial mutation-hunting software came up with quite different results,” Dr Patch said.

“This means that the second step of the process is crucial for eliminating errors and confirming which mutations are present in a cancer.

“This study lays the foundation for the coming era of cancer genomics by creating guidelines and providing new tools for achieving higher quality data, for better diagnosis and better outcomes for cancer patients.”

This study was supported by the National Health and Medical Research Council (NHMRC), the Queensland Government, The University of Queensland’s Institute for Molecular Bioscience (IMB) and the QIMR Berghofer Medical Research Institute.