Hunting for breast cancer risk with next-gen sequencing

The Hunter Medical Research Institute’s (HMRI) Pathology Service laboratory has developed DNA sequencing technology that is accelerating screening for the genetic risk of breast and ovarian cancer.

Professor Rodney Scott, the co-leader of HMRI’s Information Based Medicine research program, explained that the institute acquired funding to purchase a next-generation sequencing (NGS) system from genetics technology company Illumina. With the assistance of Dr Cliff Meldrum from The University of Melbourne, the NGS technology was married to microfluidics.

“The reason we had to do that is because for next-gen sequencing we need to amplify targeted regions that you want to interrogate, ’cos you can’t just take DNA from somebody and, without any sort of amplification, interrogate it,” Professor Scott stated.

Professor Rodney Scott and Dr Cliff Meldrum beside the sequencer.

This allowed the researchers to get a comprehensive amplification of two major genes associated with breast cancer risk - BRCA1 and BRCA2. From there, they could screen the fragments that had been amplified and look for genetic changes in them.

“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,” Professor Scott said. “We then reassemble them to make the total sequence.”

The technique is much faster than the traditional ‘gold standard’ method of Sanger sequencing, which has been in use since 1975. From a single reaction, said Professor Scott, 42 samples can be screened for both genes within 24 hours - as opposed to taking 2-3 weeks previously.

“The additional advantage of next-gen sequencing technology is the speed at which you can analyse the data, which cuts it down dramatically from several days to within about 50 minutes, thereby increasing the number of samples that you could look at at any one time and report on in that time frame.”

Professor Rodney Scott.

The method received NATA (National Association of Testing Authorities) accreditation towards the end of 2013, when the lab tested its bank of around 500 samples and matched the results with its previous data. Six months later, it has been used to screen over 1000 more women for their genetic risk of breast cancer.

“We could in fact do more - the only thing that’s stopping us is actually the supply of samples,” Professor Scott said.

As the team continues to screen patients for ovarian and breast cancer risk - about 100 samples per month - they are also hoping to broaden the method for use in other diseases.

“It has the potential to alter the way we provide medical services, in terms of identifying people at risk as opposed to reacting to people who present with disease, so that you can begin to think about seriously offering preventative measures to people,” Professor Scott said.