Handheld human genome sequencing

Just last week, scientists reported a remarkable feat of the sequencing and assembly of a human genome using the MinION (Oxford Nanopore Technologies) nanopore sequencer (https://www.nature.com/articles/nbt.4060).  The MinION is currently the only portable real-time device for DNA and RNA sequencing, weighing under 100 grams and plugging into a PC or laptop via a high-speed USB cable.  To put this in perspective, the human genome project was initiated in 1990, only a mere 18 years ago.  The project culminated in the sequencing of the human genome, after 13 years of work that included collaboration between numerous laboratories around the world, at a cost of hundreds of millions of dollars.  Clearly the technology has come an astonishingly long way in a short period of time.

The basic technology is fairly easy to understand.  In a nutshell, the MinION works via passing long strands of DNA through a tiny hole, or nanopore.  DNA is comprised of four bases, known by the letters A, C, G, and T.  When an electrical potential is established across the nanopore, as each base passes through the pore, an electrical signal unique to each particular base is generated, enabling deciphering of the DNA sequence.  However, it is well known that there are several factors that render accurate and complete sequencing of human genomes challenging.  These include large size, regions where particular bases repeat for long stretches, duplications, etc. 

Thus, the breakthrough published last week involved the development of a protocol to generate ultra-long reads (read lengths up to 882 kb), enabling sequencing of a human genome with 99.88% accuracy. 

The possibilities for future use of such technology are virtually limitless.  However, despite the breakthrough, there remains significant hurdles to overcome for the technology to become mainstream.  For example, tools to automate phasing from nanopore assemblies is needed, as are improvements to real-time base-calling in order to simplify workflow, as discussed by the scientists involved with the project. 

In summary, this is a very exciting field with room for improvements to the existing technology, and which will be very interesting to follow in terms of how particular companies approach the continued advancement of this technology space. 

Paul Focke