Faster, smaller, and organic

Update Aug 20 2012. Last week, George Church and colleagues have encoded books and images in DNA. Another use of biological material as engineering device. And one that transforms the sequencers described below in organic Kindle!

Less than two weeks ago, at the annual Advances in Genome Biology and Technology  meeting, a small company, Oxford nanopore , presented his new sequencing technology  based on … nanopores. I found that piece of news very exciting, despite working in an environment where I am force-fed next generation sequencing daily (see for instance the 1000 genomes project).

I am first excited about the new technology, because it is based on proteins. An enzyme processes the nucleic acid that is then passed to a proteic pore. The modification of electrical behaviour of the pore identifies the nucleotide. More about nanopore sequencing on Wikipedia. Biological engineering is progressively coming out of the labs where it’s been cooking for the last two decades, but we only start to imagine the effects it will have on the human society. I am a great fan of science-fiction, and science-fiction novelists played a lot with bioengineering. However, I believe they were far too conservative and the reality of the near future will make all imaginary stories pale in comparison. A USB stick size sequencing machine, built using the building blocks of life, able to sequence DNA super-quickly? Really? What next? What can now possibly be the limit? None. Synthetic biology and bioengineering will have in the first half of the XXIst century the effect that electrical engineering had on the XXth (I say first half of the XXIst century, because while I think the singularity of Ray Kurzweil is a lot of tosh, I agree with him than any tentative of prediction past then is just a waste of time). Not only are we synthesising life and producing in vitro tissues, but we will re-use bits and pieces of life for everything. Evolution and selection allow to optimise systems faster and better than engineering design, and as shown by nature around us, there is virtually no limit to what we can do with materials derived from living forms.

But the success of bioengineering is not the only aspect of the story that made my spine shivered. The size of the portable device, the MinION, is also a revolution. True, NGS allowed genome sequencing to get out of large sequencing facilities, to be installed in many research labs, in hospitals etc. But now, we are talking about bringing sequencing to everyone, everywhere, everytime.  Sequence identification and analysis will still require specific software and databases. But with the arrival of 4G, a MnION plus a smarphone will be sufficient to identify a sequence. What applications can we imagine?

  •  Metagenomics, and biodiversity studies: Investigators will be able to analyse the sequences in situ, without the need to bring back samples.
  • Epidemiology: Epidemics will be tracked on real time, allowing a greater reactivity and flexibility in the responses.
  • Immediate identification of persons: Bye bye fingerprints and iris patterns. GATTACA  is here, now.
  • [Place your favourite application here]

What does that means about genome sequence confidentiality etc? Gone down the drain. The same way we have cards identifying our blood type, we will have our genome on our ID card (or NHS card). And of course the insurance companies will have access to that. They have access to your gender as well. There is no point in keeping those aspects of you secret. In our time of social networking, our genome could even be part of our future Facebook profile. We just have to design new legal protections. Instead of saying “nobody can be discriminated based on its gender or skin color”, we should just have a generic “nobody can be discriminated based on its genome”.  There is no way we can stop that. And the earlier we get rid of this holiness of the genome, the less worried we will be.