New DNA Scanning Method Could Lead to Faster Diagnoses

Rare Daily Staff

Scientists at the University of Nottingham said they have made a breakthrough in genome sequencing, which will enable them to search for the underlying causes of diseases in human DNA more quickly than ever before.

In a new paper published in Nature Biotechnology, scientists from the School of Life Sciences at the University of Nottingham have shown that it is now possible to selectively sequence fragments of DNA more quickly and cost effectively than previously, without searching through DNA strands that are not relevant to the biological question, and reaching that answer more quickly than before.  They said the approach could have major implications in how genetic diseases are understood and diagnosed.

“In simple terms, we can now sequence the bits of DNA that we want to and ignore bits we don’t,” said Matt Loose of the DeepSeq Sequencing Facility in the School of Life Sciences at the University of Nottingham, who led the project. “The advances we present here mean we can search through and sequence regions from genomes even as large as the human genome.”

The new study shows how the team can now rapidly scan human genomes and detect genetic abnormalities using a portable DNA sequencer known as the MinION. They illustrate this by locating a change in the DNA responsible for a specific type of cancer in less than 15 hours.

A human genome has three billion data points, and a typical whole genome analysis might take several days. The team have shown that this method can now be used to ‘scan’ genomes at high speeds to see if there are obvious problems without having to sequence entire genomes, or perform elaborate lab processes to select the genomic regions of interest.
The team have developed a new selective method, called ReadFish, which allows the DNA sequencer to select just those regions of the human genome (or any genome) of interest for a specific question and so only need to use a single sequencing run.

“This breakthrough will enable us to look at a range of applications, such as rapidly searching fragments of the human genome to find evidence of genetic conditions or changes that may lead to illness such as cancer, which would have major implications for diagnosis,” said Loose. “It is already being used to identify the underlying causes for diseases in a host of different individuals for the first time.”

The latest study follows from the team’s previously published research in 2016, where they initially demonstrated the novel technique for highly selective sequencing.

In 2018, this same team led an international consortium to sequence the entire human genome on the Oxford Nanopore Technologies handheld pocket sized MinION portable DNA sequencer. At the time this required more than 40 individual sequencing runs on the portable sequencer. The technology has advanced since then.

Photo: Matt Loose of the DeepSeq Sequencing Facility in the School of Life Sciences at the University of Nottingham