4 ms·

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

rflrob 12y ago
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. [1] http://www.genome.gov/sequencingcosts/ http://www.genome.gov/sequencingcosts/
- owlmonkey 12y ago
  Totally agree with you on the computation costs. In some slides in February ONT hinted at why they had to go to a full wet sample prep and it related to input DNA amounts I believe. Their new sample prep they said allowed them to reduce their input DNA amounts to similar amounts as competitor sequencers, but without that new prep it took 10,000x more DNA to load. I guess raw DNA just doesn't load into the nanopores very easily, so it took that much higher concentration. Two years ago they claimed you could load raw blood into a chip after a 5 minute prep, but I'm guessing they will back away from that claim now since this wet chemistry is needed to get reasonable loading. This to me implies that all nanopore technology under development will encounter similar problems. They really need biological or magnetic bead processes to "load" DNA through the pores in one form or another - or else need prohibitively high DNA concentrations and amounts - so that will mean wet chemistry.
hyperbovine 12y ago
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.
- sitkack 12y ago
  How portable is a "wetlab"? Could I take this with me into the jungles of south america or the se asia?
  - rcthompson 12y ago
    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.
  - pcrh 12y ago
    A wet lab is a lab as you might imagine it on CSI, i.e. the whole nine yards. Sometimes, components of this can be miniaturized to create a "lab on a chip", but that takes another level of technological development.
  - bayesianhorse 12y ago
    It might be possible to do the preparation steps with portable gear. "Classic" DNA extraction with multiple rounds of electrophoresis or PCR aren't strictly necessary for all applications. Still, it would be easier to carry the sample back with you rather than carry the equipment into the djungle. On the other hand a lab in a developing country might have less trouble using the MinION rather than sending away the samples for sequencing.
  - 12y ago

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. [1] http://www.genome.gov/sequencingcosts/ http://www.genome.gov/sequencingcosts/

owlmonkey 12y ago
Totally agree with you on the computation costs. In some slides in February ONT hinted at why they had to go to a full wet sample prep and it related to input DNA amounts I believe. Their new sample prep they said allowed them to reduce their input DNA amounts to similar amounts as competitor sequencers, but without that new prep it took 10,000x more DNA to load. I guess raw DNA just doesn't load into the nanopores very easily, so it took that much higher concentration. Two years ago they claimed you could load raw blood into a chip after a 5 minute prep, but I'm guessing they will back away from that claim now since this wet chemistry is needed to get reasonable loading. This to me implies that all nanopore technology under development will encounter similar problems. They really need biological or magnetic bead processes to "load" DNA through the pores in one form or another - or else need prohibitively high DNA concentrations and amounts - so that will mean wet chemistry.

hyperbovine 12y ago

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.

sitkack 12y ago
How portable is a "wetlab"? Could I take this with me into the jungles of south america or the se asia?
- rcthompson 12y ago
  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.
- pcrh 12y ago
  A wet lab is a lab as you might imagine it on CSI, i.e. the whole nine yards. Sometimes, components of this can be miniaturized to create a "lab on a chip", but that takes another level of technological development.
- bayesianhorse 12y ago
  It might be possible to do the preparation steps with portable gear. "Classic" DNA extraction with multiple rounds of electrophoresis or PCR aren't strictly necessary for all applications. Still, it would be easier to carry the sample back with you rather than carry the equipment into the djungle. On the other hand a lab in a developing country might have less trouble using the MinION rather than sending away the samples for sequencing.
- 12y ago