Nanopore sequencing is a hot new technology in the science world, and when I first read about it, I thought, “Is this an April Fools’ joke?” because my lab has joked about how we want to be able to just put a pipefish into a slot and minutes later receive its entire genomic sequence. According to this News Focus article in Science (4 May 2012 issue) by E. Pennisi, “Nanopore sequencing should require little upfront preparation beyond isolating an organism’s DNA…With 20 of these machines, it should be possible to reveal a human genome sequence in 15 minutes.” Seriously??? All I would have to do is isolate some DNA and put it into the machine, and the machine will spit out the genome in a quarter of an hour???
Let me put this into perspective for everyone. I’m currently working on sequencing fragments of the pipefish genome. I’ve been working on a somewhat stubborn protocol since October, trying to optimize every step to make it as streamlined as possible. Once I get it up and running, the least amount of time it will take me to prepare my samples to be sent to the sequencer is about 1 or 2 weeks (depending on how late into the night I feel like working). This is a pretty expensive process, and then sequencing itself costs upwards of $1000 per lane used (luckily we can multiplex ~100 samples per lane, but still, it’s pricey). Then there’s the bioinformatics assembly. In order to be confident that the sequences you’re assembling are reliable, you want a high amount of coverage (redundant reads–in other words, you want to have multiple copies of each short sequence). Most of this is usually done in Linux, and basic computer programming skills are generally desirable. That’s why I’m currently learning C++.
Now, you’re telling me that I could simplify this process so that I could get the equivalent data in a day? This sounds like science fiction. But the science behind it is elegant and in many ways makes perfect sense. The basic idea is that you send a strand of DNA through what is essentially a channel that is found in the membranes of cells, and that the act of transporting the DNA through changes the ion flow and thus the electrical composition of the cell. The DNA can go through such a channel (or ‘pore’) so quickly that the developers of the technology wanted to slow it down, which they managed to do using a specific protein. And that’s the basic science behind nanopore technology! Of course, there is a 4% error rate, but this technology is still a fantastic advancement, assuming it can make it to the market. Hopefully, if it becomes as widespread as is predicted, I won’t become too bitter over all of the time I spent wasted on the old next-generation sequencing techniques.
Read more about this cool technology over at Nature, and E. Pennisi discusses the future of Nanopore sequencing in Science. Additionally, if you want to listen to a podcast discussing nanopore sequencing, Elizabeth Pennisi discussed it on the 4 May 2012 Science Podcast. Nature also has a summary of the other current sequencing technologies, for anyone who’s interested.