Sequencing so fast you’ll think you’re on CSI:
If you’ve ever watched a procedural crime-solving show on television, you’re sure to have seen a lab tech magically produce results from a complicated assay in mere minutes. If you’re a wet lab scientist, you’ve probably found yourself wishing that “CSI technology” were real so you didn’t have to spend your whole day running PCRs and gels.
In this month’s issue of GENETICS, Wei and Williams, from the Montefiore Medial Center at the Albert Einstein College of Medicine, use sequencing technology that seems akin to science fiction to rapidly detect aneuploidy in just hours – an advance that could greatly improve the current state of clinical sequencing.
The study features the minION – a nanopore-based sequencer that reads and records DNA sequence in real time from very long reads. The minION sequencer is small – not much bigger than a USB thumb drive – and plugs directly into the computer that will be used to analyze the data. Inside the sequencer, nanopores create channels for DNA or other molecules to pass through a membrane that has an electric potential. When molecules pass through the nanopores, they disrupt the potential in a characteristic manner, which gives a known pattern in the read-out that lets them be identified. (Oxford Nanopore Technologies has an excellent animation explaining the technology in detail here.)
Wei and Williams developed a sample preparation and data-analysis method that uses the minION sequencer to produce rapid, real-time sequencing of short pieces of DNA, a change from the extremely long reads originally used in nanopore sequencing. Their methodology allowed them to detect aneuploidy, including trisomies and sex-chromosome abnormalities, in prenatal and miscarriage samples in less than four hours.
This methodology could potentially allow clinicians to detect aneuploidy in time-sensitive samples in just a few hours, for less than a thousand dollars – something that could only have been dreamt of even a decade ago. With exciting new methodologies, science fiction is on its way to science fact, and it’s picking up speed all the time.
Wei S., Williams Z. 2016. Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology. GENETICS, 202(1):37-44. doi: 10.1534/genetics.115.182311 http://www.genetics.org/content/202/1/37