Oxford Nanopore MinION – USB stick-sized DNA sequencer
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Oxford Nanopore MinION – USB stick-sized DNA sequencer
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Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#2What does it mean? I don't suppose I can put a drop of blood onto that sequencer and receive a sequence?
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#3What does it mean? I don't suppose I can put a drop of blood onto that sequencer and receive a sequence?
In theory you could, at least according to the hype. You would probably be better off taking a drop of blood, mixing with various reagents to lyse the cells and lightly fragment the DNA, but that's the dream.
Of course, thanks to the accelerated Moore's law that applies to sequencing over the last couple decades [1], it'll probably be the case that the computer power will be more expensive than the actual sequencing.
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#4What does it mean? I don't suppose I can put a drop of blood onto that sequencer and receive a sequence?
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.
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#5What does it mean? I don't suppose I can put a drop of blood onto that sequencer and receive a sequence?
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 sequ…
How portable is a "wetlab"? Could I take this with me into the jungles of south america or the se asia?
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#6Very 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.
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#7Earlier quoted context omitted.
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 sequ…
How portable is a "wetlab"? Could I take this with me into the jungles of south america or the se asia?
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.
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#8The 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.
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#9Looks 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!
Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer
#10The 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…
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.