Researchers at CSIRO’s Australian e-Health Research Centre have developed a more powerful way to find the genes that cause disease, bringing us a step closer to better diagnosis and treatment of genetic diseases.

The new software, detailed in a paper just published in Scientific Reports, offers a more reliable way to recreate gene mutations in the lab.

Dr Denis Bauer, CSIRO Transformational Bioinformatics Group Leader and corresponding author on the paper, said the software makes HDR-based nucleotide editing 83 per cent more efficient.

“A single misspelling in the three-billion letter long human genome can cause life-threatening diseases such as cystic fibrosis,” Dr Bauer said.

“To understand which genomic mutations cause specific diseases, researchers have to recreate these mutations in the equivalent gene in the lab – traditionally a labour-intensive and slow process, limited to diagnosing disease rather than treating it.

“Using artificial intelligence, we’ve developed software that makes HDR-based editing 83 per cent more efficient, providing a much faster and more powerful tool than the existing base-editing technology.”

Dr Bauer said researchers use base-editing to mutate specific letters in the genome, but this method can only be used for some changes, such as changing a “C” to a “T” but not an “A”.

“HDR-based nucleotide editing provides a custom DNA template to copy, allowing researchers to make any change they need – but it’s never been a reliable option before now,” Dr Bauer said.

“Our software is the first software tool to support HDR-nucleotide editing and make it a more reliable editing tool.

“We hope it will make it easier for researchers to understand the genomic causes of diseases to develop cures and treatments – and accelerate the human race’s understanding of how the genome really works.”

The new cloud-based web service software, known as CUNE, is the result of a collaboration between CSIRO and the John Curtin School of Medical Research at the Australian National University. To find out more about the software or enquire about collaborating with the team, contact Dr Bauer at

O'Brien et al. Unlocking HDR-mediated Nucleotide Editing by identifying high-efficiency target sites using machine learning Scientific Reports 2019