
Oxford Nanopore MinION – USB stick-sized DNA sequencer - bayesianhorse
http://nextgenseek.com/2014/06/behold-oxford-nanopore-reads-are-here/
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dnautics
The error rate in the "good part" is about 15%. That is quite frankly very
very very poor. This might be a good alternative to pacbio, (unless the other
technologies can increase their read lengths).

Typically (I chatted with my contacts at the Venter Institute)... best results
are gotten by making long reads using pacbio or (maybe minion, they are
looking into that currently) and using that to generate the scaffold and
miseq/iontorrent to fill in the rest.

Honestly in my opinion (and I have been saying this for years) Pacbio and
minion will never get over their error rate for "basic chemistry" reasons.
These techniques use single-molecule sequencing and that is fraught with
problems. Sometimes, it's better to average over a large population.

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dnautics
More information: For personal (as in human genome) sequencing, I'm not
entirely sure how useful this is... We already have a scaffold for the human
genome (that would be Mr. Venter himself) and MAYBE you could get some haploid
information out of it, but you'd worry that the base pair you care about for
any given individual is in one of the wrong stretches.

For organism sequencing, I think this could be even worse than pacbio; there
are modestly sized gaps in the sequence compared to relative to the known
pseudomonas sequence; imputing the correct sequence when you have _no
available template_ is going to be a nightmare. It's easy to say "15% error"
when you know what the 100% correct result is. But if you have no reference
correct sequence and all of your parts are up to 15% wrong, the difficulty is
compounded.

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petercooper
Naive idiot alert.. could you process the "same" DNA numerous times then take
the mode in each case? Or are the errors essentially ones that would be
repeated each time?

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mbreese
Actually PacBio does just that to get better a better error rate. They
basically have X amount of sequencing that can be done. You can spend that X
however you'd like. If you want a sequence that is X long, you'll have a
higher error rate. If you want a chunk that is X/10 long, you can circularize
it, and thus sequence it ten times. This gets you better accuracy with the
redundancy. DNA is pretty robust.

In practice though, even with these "circular consensus sequencing" reads, the
error model is significantly higher than other technologies.

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njbooher
I don't think they push CCS much anymore. The focus seems to be on generating
long reads and then using Quiver to call the consensus
([https://github.com/PacificBiosciences/GenomicConsensus/blob/...](https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/QuiverFAQ.rst)).

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mbreese
That's probably wise of them. The last time I looked at data from them, the
CCS reads were still very noisy. It's better to rely on your strengths. In
their case, it's long reads.

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njbooher
Yup. Just keeps getting better
([https://pbs.twimg.com/media/BpUs_MAIYAEHb2o.png:large](https://pbs.twimg.com/media/BpUs_MAIYAEHb2o.png:large)).

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ihodes
The error rate of 15% (I actually believe it's more like 30% in practice,
which is 2x PacBio's) is actually excellent and comparable to PacBio's in that
the error is primarily randomly distributed, and not systematic like current
Illumina or IonTorrent systems (which have admittedly lower error rates, at
1-3%). The short of it is, absolute error rate is not the whole story.

When looking at what ends up being just a massive string of 4 characters,
having 15% error on a particular read doesn't matter _too_ much; you end up
getting many reads (fragments of a full sequence) which overlap the same area
of the genome. With enough reads (and having many, say 15-100x coverage as
it's called, is not uncommon practice in sequencing), this error is obviated
by consensus. The long read length is especially useful for this, as the
lengths which overlap are much greater than with current NSG reads of
150-200bps.

Additionally, I think the goal of the MinION were more to display a sort of
disposable (sub-$500) machine which could be used on-site and without sample-
prep. A forensic kit, really (though probably more for creatures such as
bacteria and fungus rather than humans—I recall that it would take 2-5 MinIONs
to sequence a human genome to even a short depth, but I may be
misremembering).

In short, this is a cool proof-of-concept for Oxford Nanopore, as their
technology has been talked about for a long time with nothing to show until
now. It will be interesting to see where it goes next, particularly if the
reads lengths keep climbing and the error profile drops even more.

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pcrh
As it stands, it looks good enough for identification purposes (for example of
a pathogen), but nowhere near good enough for genetic studies where single
base pair variations are the most sought-after aspect.

For human genetic studies, I guess it also depends on how readily multiple
reads can be obtained, and whether the errors are randomly distributed.

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owlmonkey
Totally agree. It is at best a semi-portable sensor (with wet prep) not a
sequencer. Cost would be another big obstacle for using MinIon on human data.
At about 100 megabases and $1000 per cell that's three orders of magnitude
more expensive per base than a HiSeq X. (edit: spelling)

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tkinom
Very nice! I worked on the firmware for the "Applied Biosystems ABI Prism 310
DNA Sequencer". I remembered it cost >$60K each when it was released ~1996,
1997 time frame.

It is good to see DNA sequencer tech progress faster than Semiconductor.

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kanzure
> I worked on the firmware for the "Applied Biosystems ABI Prism 310 DNA
> Sequencer".

Do you have copies of that firmware or know where I could pick it up? I'd like
to poke around, try some reverse engineering, etc.

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tkinom
Sorry, it was not open source. BTW, it is just standard embedded firmware that
control 3 axis motors + pump, CCD camera, etc. Highly couple to that
particular instrument' HW. I am not sure what you can learn from it even if it
was open source.

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waiquoo
I would like to see what the real raw data looks like. There doesn't look to
be any noise in that wiggle plot and the signal has already been processed to
a degree (see the hard edges and squareness of the features). That's really
the hard part though, going from raw to digital, and the decisions that are
made regarding how that transformation is achieved will have a lot to do with
the quality of the data.

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facepalm
What does it mean? I don't suppose I can put a drop of blood onto that
sequencer and receive a sequence?

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hyperbovine
No, it does not. You still need a wetlab to do sample preparation. There are a
couple reasons why this is exciting though. Oxford Nanopore has seemed like
bogus vaporware for several years now, and many people were skeptical that
they had a viable product. This data release is the strongest suggestion yet
that the thing actually works (but is still in no way conclusive). Two,
assuming it does work, being able to sequence 5-10kb fragments will be a game
changer for decoding complex structural variation and repetitive regions of
the genome. Current sequencing technology (read lengths on the order of
100-200bp) is simply not up to the task, and yet tons of interesting phenomena
are believed to be hiding out in those regions. For example, there is mounting
evidence that telomere shortening is strongly associated with aging. Existing
NGS machines are powerless to interrogate telomeres in humans, because they
consist of several kilobases of the repetitive sequence TTAGGG. If Oxford
Nanopore's claims hold true you could in theory sequence the whole thing in
one go. Being able to do this would advance our understanding of aging by
leaps and bounds, I suspect.

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sitkack
How portable is a "wetlab"? Could I take this with me into the jungles of
south america or the se asia?

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rcthompson
A wetlab doesn't refer to any specific set of equipment. It refers to all the
stuff that you do that involves transferring liquids between test tubes via
pipets, heating and cooling them, etc., in contrast to "dry lab", which refers
to computational data anlaysis. Depending on the type of sample, the wetlab
preparation will vary. For example, if you have an extremely small amount of
starting material (e.g. you want to sequence the DNA of individual cells), the
prep will be different, or if you want to sequence RNA from blood, you need a
step to remove all the mRNA that encodes hemoglobin, which is 50-75% of the
total mRNA.

I do dry lab exclusively, so I'm not sure what the most bsaic sample prep
procedure consists of, and whether the equipment needed for that prep can be
made portable. But in the field, you're going to have to contend with
contamination issues, since tiny amounts of contaminating DNA can mess things
up big time. I don't think you can just carry around a portable autoclave, so
maybe the solution would be individually-wrapped sterile prep kits, maybe with
the possibility to sterilize, reset, and re-wrap them back at home.

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davecap1
Looks like we're getting pretty close to solving the sequencing problem... the
next massive challenge is in using genetic code to actually understand health.
If you're an engineer looking for some meaningful work, SolveBio wants to hear
from you!

