
After Long Delays, Breakthrough Nanopore Sequencer Finally in Labs - rberger
http://www.technologyreview.com/news/530746/radical-new-dna-sequencer-finally-gets-into-researchers-hands/?utm_campaign=newsletters&utm_source=newsletter-daily-all&utm_medium=email&utm_content=20140917
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waiquoo
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...](http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12324/abstract)).

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.

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troymc
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?

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waiquoo
Winston Timp has done some interesting work in this area
([http://www.sciencedirect.com/science/article/pii/S0006349512...](http://www.sciencedirect.com/science/article/pii/S0006349512004511)).
Basically, by training a hidden Markov Model, you can get the most likely
sequence from a noisy source.

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Sulfolobus
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...](https://www.youtube.com/watch?feature=player_detailpage&v=UtXlr19xTh8#t=189)

\- 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...](https://www.youtube.com/watch?feature=player_detailpage&v=UtXlr19xTh8#t=2950)

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jacquesm
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).

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

[http://www.economist.com/news/technology-
quarterly/21615029-...](http://www.economist.com/news/technology-
quarterly/21615029-george-church-genetics-pioneer-whose-research-spans-
treating-diseases-altering)

"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."

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Gatsky
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...

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nhstanley
Here is a critique of this system by an expert:
[http://omicsomics.blogspot.com.es/2014/09/reanalysis-lays-
ba...](http://omicsomics.blogspot.com.es/2014/09/reanalysis-lays-bare-minion-
reviews.html)

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

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XorNot
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.

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

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

~~~
waiquoo
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.

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geographomics
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.

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

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

