Novel device allows selective DNA sequencing in real time

London

Using a novel technique, scientists have demonstrated for the first time that it is possible to selectively sequence fragments of DNA in real time, thus greatly reducing the period needed to analyse biological samples.

"This is the first time that direct selection of specific DNA molecules has been shown on any device. We hope that it will enable many future novel applications, especially for portable sequencing," said Matt Loose from University of Nottingham.

Called MinION, the new device was used with real-time nanopore sequencing to enable the user analyse only DNA strands that contain pre-determined signatures of interest. 

"This makes sequencing as efficient as possible and will provide a viable, informatics based alternative to traditional wet lab enrichment techniques. The application of this approach to a wide number of problems from pathogen detection to sequencing targeted regions of the human genome is now within reach," Loose added in a paper described in the journal Nature Methods.

The pocket-sized device — the same technology which NASA recently sent to the International Space Station (ISS) in an effort to investigate whether DNA sequencing is possible in microgravity — employs tiny molecular pores in a membrane that 'sense' the sequence of DNA fragments passing through these nanopores, producing minute fluctuations in a current trace.

These current traces, termed "squiggles" then need to be converted to DNA bases using base caller software, often located in the cloud. The team used signal-processing techniques to map these squiggles to reference sequences, by passing this step.

The researchers showed that this "real-time selective sequencing", or as some have called it "DNA testing", can reduce the time needed to sequence key DNA fragments or enable the analysis of pathogen samples where there is host and other DNA present in the sample. — IANS