Global cancer genome project releases first data

In October 2007, cancer researchers from around the world gathered together to embark on an epic quest to sequence 500 genomes from each of 50 different types and subtypes of cancer.

Now, two and a half years later, the International Cancer Genome Consortium (ICGC) has released its first results, including data produced by researchers at the University of Queensland and the Garvan Institute on pancreatic cancer.

Writing a Nature paper published today, the Consortium expects to see hundreds of individual cancer genomes published this year, with thousands more each year after that, all made available free on the internet to the general public and researchers.

Australia's contribution to the ICGC comes in the form of sequencing pancreatic cancer, the forth most common cause of cancer death in Australia.

The research is led by Professor Sean Grimmond from the University of Queensland's Institute for Molecular Bioscience in Brisbane and Professor Andrew Biankin from the Garvan Institute of Medical Research in Sydney.

“This is already revolutionising the way we do cancer research,” said Professor Biankin, who helped co-author the Nature paper.

The data will help in the push towards personalised medicine, where each cancer can be targeted based upon its specific genetic profile rather than the current treatment method of applying individual therapies until one is found to be effective, by which point the cancer may have advanced.

“The problem we have is the complexity of cancer. No two tumours are the same, even within the same type of cancer. They may look the same under the microscope, but their molecular aberrations vary greatly.

“When we treat a cancer, we give a person the drug that’s most likely to work – within the limitations of our current understanding. The drug may not work for that individual, even though it works for the majority of patients with the same kind of cancer.

"If the treatment fails, we go onto the second-line treatment, which might also fail. By the time we get to the treatment that’s actually going to work, it might be third or fourth down the line and the cancer may have advanced. In the case of pancreatic cancer, the patient has probably died.

“The consortium’s internet-based databanks will help us treat specific cancers with specific treatments. Not only that, the information will help us understand why some treatments work and others do not, and then design better drugs to target faulty elements or mechanisms,” he said.

The first genome sequences for pancreatic cancer have already revealed some surprises for the researchers.

“We’ve just done a handful of sequences – and already we know for sure that real cancer looks substantially different from the cell lines we’ve been using in the lab,” said Biankin.

“We’ve hypothesised about that in the past, but having the evidence to prove the difference is exciting. Right from the outset we know everything there is to know about one person’s tumour at the genomic, transcriptomic and epigenomic levels. We might not understand it, but we’ve got the data.”

Along with the pancreatic cancer data, other international groups have also published their own contributions to the ICGC, including data from the UK, Canada, Japan and the US on breast cancer, liver cancer, serous cystadenocarcinoma of the ovary, a whole metastatic melanoma cell line as well as links to the single nucleotide polymorphism database (dbSNP) and the HapMap databases, providing access to common patterns of variation in reference population samples.

Australia's contribution also involves contributions from the Walter and Eliza Hall Institute of Medical Research, Johns Hopkins University in Maryland, the Ontario Institute for Cancer Research, the University of Verona and the University of California, San Francisco.

The project is funded care of $27.5 million from the National Health and Medical Research Council of Australia (NHMRC), which is the largest single grant the NHMRC has ever awarded. It is also supported by The Cancer Council NSW, the Queensland Government, the Garvan Institute and the University of Queensland.

Applied Biosystems and Silicon Graphics are also making significant contributions.

The paper was published in Nature (doi:10.1038/nature08987) today.