Cancer risk diagnosis ‘turbo-charged’ by new sequencer

Apr 9 2014

Professor Rodney Scott, left, with Dr Cliff Meldrum and the NextGen sequencer.

An HMRI genetics laboratory at Newcastle’s John Hunter Hospital has become the first in Australia, and one of the few in the world, to receive accreditation for a new diagnostic system that revolutionises ‘NextGen’ DNA sequencing for breast and ovarian cancer.

Employing cutting-edge technology, researchers are able to process samples from up to 40 patients simultaneously instead of individually, and where data analysis previously took three hours per person it now takes just 10 minutes.

“To screen 1000 women for a study would take 18 months with the old technology whereas we could now do it in six to 10 weeks using the new sequencer,” Professor Rodney Scott*, from the University of Newcastle, said.

“That means an awful lot to people working in the lab, but more importantly it will allow more women to have access to genetic testing and give more timely results to reduce their stress.”

It comes as public awareness and demand for BRCA1/BRCA2 gene testing has escalated in the wake of actress Angelina Jolie’s decision to have a double mastectomy.

Professor Scott secured an Australian Research Council grant to buy the new sequencing unit and at the same time lured pathologist Dr Cliff Meldrum back to the Hunter from a Melbourne institute. It took a further two years to perfect the system.

“The combination of Cliff’s technical ability and the right technology set the scene for our lab being appointed the first NATA [National Association of Testing Authorities] accredited facility in the country to test for breast and ovarian cancer susceptibility using this approach,” Professor Scott said.

“We were able to successfully complete a validation study looking at 400 to 500 samples that had previously been tested by the standard methodology.

“It now provides a quantum leap in our ability to provide a service to patients, and is a perfect example of technology from a research lab environment being translated into a clinical utility.”

Dr Meldrum says the new process is not only less labour-intensive but also more cost efficient as it has the ability to quickly analyse large data sets.

“The two genes, BRCA 1 or BRCA 2, are both large so we break them into around 180 fragments and find the DNA sequence of each fragment. We then reassemble them to make the total sequence,” he explained.

“To handle 40 or so samples at once, we insert synthetic DNA barcodes onto the end of each sample. They all end up in a single tube, which is mind-boggling.”

Professor Scott is confident the sequencer can now be utilised for further clinical applications.

“This is the proof-of-principle,” he said. “We move from here to other familial cancer syndromes such as colorectal cancer testing, and other non-cancer applications will flow beyond that.”