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Opening the doorway to cancer data


Precision medicine is offering hope to cancer patients. The power of genomics and the masses of data it creates is transforming cancer research and allowing personalised treatments with more proven effects.

Genome mannequinLike hundreds of other cancer researchers, Mark Ragan and his team at The University of Queensland's Institute for Molecular Bioscience (IMB) need to design experiments based on data from human and cancer genomes. Using data chips and next generation sequencing they must assemble their genetic data, interpret it to understand what genes their data refer to by comparison with other samples, and then classify patients' cancer into subtypes. If they can't match to an existing subtype, they identify a new one. Ragan says this intensive work requires access to as much genetic data as possible.

"It would literally be impossible without access to data from thousands of cancer genomes."

Luckily, there are portals with this type of data. One of the first to start collecting cancer genome data was the The Cancer Genome Atlas (TCGA). The initials TCGA also make up the four-letter code of nucleotide bases thymine, cytosine, guanine and adenine that DNA uses to 'write' genetic information.

TCGA was started by the US National Institutes of Health (specifically the National Cancer Institute and the National Human Genome Research Institute) in 2006. Ragan says its initial goal was to generate data from researchers across research institutions on two cancer types. Early success expanded the initial goal to collect and profile more than 10,000 samples from over 20 tumour types. While the sample collection phase ended in 2013, data reuse ensures the data generated from those samples are still being analysed. Over 2700 papers have been published by TCGA data so far, including Australian researchers.

The data portal for the TCGA is "amazing" says Ragan. "It's a really powerful portal that lets you ask questions and interrogate gigantic amounts of cancer genome data, including sequences, survival rates and subtype classifications."

"Just about everything in it is open access, and the raw data, which isn't open access, is made available by applying through research institutions' ethics committees."

New initiative

A newer initiative inspired by the success of TCGA, the International Cancer Genome Consortium (ICGC), is an international project in which Ragan's colleagues play a part. ICGC is built on the TCGA project, which provides about 60% of the patient data in ICGC's Data Coordination Center. ICGC aims to cover 50 tumour types and currently funds 78 international cancer genome projects like the Australian project at IMB.

"Our research into breast cancer subtypes and survival would literally be impossible without the data reuse that TCGA and other genome research programs offer. We can tell if we've discovered a new cancer subtype or not, or even whether the existing data need reinterpreting," says Ragan.

Knowing a patient's cancer subtype allows more tailored, evidence-based treatment, potentially increasing patient survival rates and quality of life by allowing clinicians to more confidently focus on prescribing the drugs most likely to succeed for a particular patient.

One of the exciting things Ragan and other researchers are finding from the data is that some quite different cancer types have a similar genetic basis. This means drugs to treat one type of cancer, such as breast cancer, could be used for another, such as ovarian cancer.

"Instead of waiting 10 years for a new drug to be developed, patients may be able to be treated straight away with a drug that's already available for another cancer," says Ragan.

That's good news for patients, and it also makes drug development, which can cost hundreds of millions of dollars per drug, more cost-effective. This potentially creates a larger market for a given drug, and makes some drugs financially viable that otherwise wouldn't get to market.

Story provided by Refraction Media.

Image: Genome mannequin courtesy of Greyloch (Creative Commons / Flickr)

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