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Largest ever release of child cancer genome data boosts research

06 June 2012

By Dr Victoria Burchell

Appeared in BioNews 659

A wealth of whole genome data – or the entire genetic code – from children with cancer has been released by scientists in the US. The researchers claim the database more than doubles the volume of highly detailed, whole genome data available worldwide.

The data has been generated as part of the three-year Paediatric Cancer Genome Project (PCGP), a collaboration between St Jude Children's Research Hospital in Memphis, Tennessee and Washington University. So far the project has sequenced the DNA of 260 children with cancer, and by the year end that number is expected to reach 600.

Two samples have been sequenced from each patient: one from the tumour; the other from healthy tissue. By looking for differences between the healthy cells and the cancer cells, the scientists hope to identify the mutations that cause the cancers.

The project, which cost an estimated $65 million, is the first privately funded study of its kind to make its data freely available.

Dr William Evans, CEO and director of St Jude Children's Research Hospital called the PCGP 'a one-of-a-kind effort, so the information has the potential to accelerate disease research worldwide'.

Improvements in the early detection of childhood cancers have raised survival rates over the past two decades, but treatment continues to rely on conventional approaches which often have severe side effects. By identifying the mutations that cause the cancer, scientists hope it will be possible to target drugs directly to the root of the problem.

Unlike many studies which only look at certain regions of the genome, the PCGP researchers have analysed the entire sequence, including DNA that does not code for proteins. This allows the researchers to identify more unusual, 'cryptic' changes which would not otherwise have been found.

The project has already yielded results which are published in the journal Nature Genetics. An aggressive form of acute lymphoblastic leukemia (ALL) was shown to be genetically closer to acute myeloid leukemia (AML) rather than other lymphoblastic leukemias. Treatments for ALL and AML are very different, so treating this form of ALL with AML drugs may be an approach worth investigating.

Another surprising finding was that cancer of the retina (a part of the eye) could be traced to a single gene, SYK. Expression of SYK was altered in every retinal tumour analysed, and an existing cancer drug targeting the gene shows promise in early lab tests, researchers say.

Speaking to Time magazine, Dr James Downing, scientific director at St Jude, said: 'There is a wealth of information that we are generating and it will take years to extract all the valuable information. But we need to start by getting it out into the hands of everybody in the scientific field – not only those in cancer research – so they can used it both as a reference and as a discovery tool, and find new things that we have yet to find'.

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