After Long Delays, Breakthrough Nanopore Sequencer Finally in Labs | Hacker News Reader

After Long Delays, Breakthrough Nanopore Sequencer Finally in Labs

technologyreview.com

45 pointsrberger16 comments

Researcher working on a different approach to nanopore sequencing here. The Minion is really interesting technology, but early reports basically indicate that it's essentially useless in it's current form. One of the issues is that the basecalling algorithm relies on a noisy, two bit signal. Apparently it works okay on trained sequences, like lambda DNA (that's where the 60-85% accuracy comes from). But when used to sequence untrained DNA, the accuracy drops off significantly (<10% accuracy, http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12324/a...).

There is lot's of room for improvement though. All of the commercial nanopore tech is based on biological nanopores, which have the advantage of having very straight-forward to fabricate. But they are limited to the ionic current signal, which is very noisy and weak. Once these companies start introducing solid-state devices though, things will begin to get very interesting as alternative signal transduction mechanisms come into play.

It sounds like they are reading several DNA strands in parallel at the same time, and each output-sequence has noise. It seems to me the problem then becomes one of finding the most probable "signal sequence" given all those noisy output-sequences. Oh, and it also sounds like you wouldn't know which letter is number 1, which is number 2, etc. Is that right?

It seems like a fun problem in information theory. Can you point us to some articles or papers about current approaches to solving it?

Winston Timp has done some interesting work in this area (http://www.sciencedirect.com/science/article/pii/S0006349512...). Basically, by training a hidden Markov Model, you can get the most likely sequence from a noisy source.

There was recently an online mini-conference mostly about the MinIon (involving the CTO of Oxford Nanopore and a few of the researchers involved in the MinIon Access Program).

People may be specifically interested in the first and second talks with the corollary of both being likely biased towards the MinIon:

- 1st is by Clive Brown (ONP CTO) and discusses the MinIon platform, background to the Nanopore technology, analysis platforms and the future PromethIon expansions - https://www.youtube.com/watch?feature=player_detailpage&v=Ut...

- 2nd has Nick Loman (one of the MAP researchers but admitted 'fanboy') discussing the performance on the MinIon in his lab in 'real world' conditions - https://www.youtube.com/watch?feature=player_detailpage&v=Ut...

This is one of those examples where both patents and venture capital come out shining.

Incredible work, the stamina on display is extremely impressive and I hope they and their backers will reap the rewards from all the hard work very many times over.

To put in laymans terms what this thing is: it's a tape-playback machine for DNA.

Now they need to fix the bugs (hard, but probably not nearly as hard as getting to this stage in the first place).

Talk about serendipity, I was just reading this article from September 6th:

http://www.economist.com/news/technology-quarterly/21615029-...

"One of these, Genia, is commercialising a process called nanopore sequencing that Dr Church first devised in 1988. Distinct polymer tags are attached to each of the four nucleotides poised to contribute to a single molecule of replicating DNA. As they react, the tags are released near a protein layer full of tiny holes called nanopores. Each tag blocks the flow of electrical ions across the layer in a different way. Because it relies on electronics rather than optics, nanopore sequencing promises faster, cheaper sequencing. Dr Church holds up a fingernail-sized chip containing 128,000 nanopores that he reckons will bring the cost of sequencing down to $100. In June, Genia was acquired by Roche, a Swiss pharmaceuticals giant."

Not having to deal with all the complexities of analysing short read sequence data would be fantastic, I hope they get the accuracy a bit better. At the moment current sequencing technologies are great at detecting mutations but struggle with changes in gene number, gene fusions and large structural variation at the kilobase or more scale. Hopefully long read tech will open up this aspect of genomic information to greater scrutiny.

Having said that, for cancer genomics, the vast majority of archival tumour tissue in the world is stored in a way that auto-fragments the DNA, so being able to do long reads won't actually help...

Here is a critique of this system by an expert: http://omicsomics.blogspot.com.es/2014/09/reanalysis-lays-ba...

It's a great achievement and I'm hopeful, but the accuracy needs to go up before it competes with current standard.

At $1000 a machine, if they can get the accuracy up these things are going to be everywhere. There'll be absolutely no reason for any lab tangentially related to DNA not to have one.

Like that is not even a blip in a normal research budget for equipment.

I like that it is called a Minion. Presumably there is a gene sequencer market for evil megalomaniacs who live under volcanoes.

How do they get the DNA unwound and free from tangles? Isn't it normally wrapped around his tones ?

There are a number of ways to handle that problem. You could melt the DNA or denature it in a basic solution. In some nanopore designs, the diameter of the nanopore is so small that when the DNA is pulled through, only a single strand can pass which forces the DNA to unzip and untangle. I believe the Oxford Nanopore approach is to use an enzyme to cleave single nucleotides off of the end of the strand one by one. That way the signal is only coming from a single base, which is helpful in the decoding process.

The DNA would have to undergo purification beforehand anyway, to extract it from the cell and separate it out from the cellular proteins and RNA. So histone removal would be through modified salt concentrations and protease action.

Also I think the method you are describing is their other sequencing approach - this one, as far as I know, passes an intact strand through each pore and examines the electrical conductivity of overlapping 6 base pair sequences.

How do they pull the DNA through the pores? That just seems impossible to me.

In solution, DNA is weakly charged. The application of an electrical potential across the pore threads it and pulls it through.

I think the sequences are first prepared by attaching a motor protein at the ends of the strands.

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