Tag Archives: Australian researchers

Rapid detection tool

Australian researchers develop Big Data tool to test new medicines

Australian scientists have developed a rapid detection tool to map the effects of new medicines already on the market, potentially saving millions of health practitioners from prescribing medicines with lesser-known yet serious side effects.

Lead researcher Dr Nicole Pratt, a senior research fellow at the University of South Australia‘s School of Pharmacy and Medical Sciences, has been working with the Asian Pharmacoepidemiology Network (AsPEN) to develop a mathematical algorithm that charts the temporal relationship between a new medicine and reports of adverse side effects around the globe.

“At the time a new medicine is first released onto the market less than 50% of the side effects are known.”

The rapid detection tool is able to quickly analyse large population datasets of up to 200 million people, containing information about the time a patient is prescribed a new medicine (captured at the point of purchase) and recorded hospitalisation events.

“We look at the link between starting a new medicine and a hospitalisation event and determine whether there is an association between those two events,” says Pratt.

At the time a new medicine is first released onto the market less than 50% of the side effects are know.

On average, new medicines are tested on less than 2000 people before they are prescribed – too few to determine if rarer, serious side effects exist.

Pratt’s rapid detection tool has the potential to become a real time surveillance tool for drug administration bodies, researchers and general practitioners, helping them to identifying the effects of new medications before they lead to widespread complications.

“We’d like to see it reach the point where we are constantly looking at the data and trying to capture problems as soon as they happen rather than let them happen for years and years and then do a big study to find that there have been a whole heap of heart attacks.”

The tool is already being used in several countries, including Japan, Korea, Taiwan, Canada and Australia to look at the side effects of a heartburn medication prescribed for reflux, and a medication for diabetes associated with heart failure.

In analysing the populations’ use of the heartburn medication, “all of the datasets found very similar results in terms of this medicine causing serious gastrointestinal infections,” says Pratt.

But when they analysed the diabetes medication, Pratt says they started to see differences between the five countries, indicating the drug might have a different effect on people depending on their ethnic background.

“When we looked at the association in the Asian population, we weren’t able to see the effect, but when we looked in the Caucasian population in Australia and Canada, we found the association.

“So the application is to start to look at whether there is some genetic differences in the way people respond to medicines and know what the risks and the benefits might be across ethnicities,” she says.

One of the challenges Pratt faced in developing the highly mathematical tool has been making it accessible for more people.

She says UniSA Professor Libby Roughead has been instrumental in helping her to apply the numerical tool visually in a “real-world” healthcare setting.

At the moment, “the datasets are held by either the governments or the hospitals in each of the countries, but the actual output of the tool should be available to general practitioners, scientists and regulators,” says Pratt.

“So what we are trying to do is visually provide an output to the people who are going to use it at the point of prescribing medicines.”

“Some of the things we’ve been trying to do is look at how the data can tell you stories, rather than just give you numbers.”

At the moment the tool produces a visual graph charting when medicines are prescribed and superseded across populations, while highlighting peaks in adverse effects at certain points in time.

“I’d like to see s this work integrated into the regulatory systems of all these countries and make it a world-wide surveillance system.”

Pratt met with her colleagues from AsPEN in Thailand this week, to discuss the global expansion of the rapid detection tool.

This article was first published by The Lead on 24 November 2015. Read the original article here.

Doorway to cancer data

Precision medicine is opening the doorway to cancer data and 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.

Like 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 genetics. 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 the data reuse that TCGA and other genome research programs offer”

Doorway to cancer data

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.

Doorway to cancer data
Photo by Richard Ricciardi.

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.”

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.


New treatments

Knowing a patient’s cancer subtype allows more tailored, evidence-based treatment, potentially increasing 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.

Originally published in Share, the newsletter magazine of the Australian National Data Service (ANDS).