5 ms·

The first DNA 'tricorder' in your pocket

43 points by dnetesn 6y ago

TomJansen 6y ago
I didn't realize that they were this far with Nanopore technology. Really awesome stuff. The weird thing in this article is that they say that "Most of the studying of DNA: aligning, analyzing, is done on large server clusters or high-end laptops." but that an iPhone app can replace that. In my experience, aligning is not computationally intensive at all.
- koeng 6y ago
  Aligning doesn’t, but basecalling seriously does. The best base callers are still big machine learning models that take quite good GPUs
rapjr9 6y ago
So, can this be used to track where people have been? Follow the plume of DNA from the skin cells they shed? Is it an immediately useful way to tell if someone has COVID-19? Could it be used to covertly build a database with a unique DNA ID for all people? How fast is it, how much does it cost, are there consumables that have to be replaced? Some answers here: https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies https://nanoporetech.com/ https://nanoporetech.com/ This does not seem to bode well for privacy.
- dmos62 6y ago
  It's sad that our privacy and hence well-being is so intimately threatened by technological progress. It says something about the powers that be. In the ideal setup, we'd only be thrilled by new technology, while legislature and its enforcement would regulate things that might harm us, like tracking.
- amelius 6y ago
  > So, can this be used to track where people have been? The same can be said about cameras. And DNA tracks are easier to fake.
- koeng 6y ago
  Yea, you can use it for COVID19 diagnostic tests. I did that back in April-ish for a project before they redirected the Nanopore reagents to commercial COVID testing. Yes, it could be used to build a database, so long as you have a good amount of DNA from the person. Honestly, governments are already doing this with Illumina runs, so no diff there really. It immediately generates runs, and tapers off at about 12-24 hours, and using a full flow cell takes like 48. How long you run it for depends on depth of reads. Flongle flow cells cost $99 and approximately $200 at end of day and minion flow cells cost about $1000, with minion being about 10x as good as flongle. The primary cost is definitely consumables, the capex for these devices is very low.
helsinkiandrew 6y ago
Not to be picky but did the Star Trek tricorder sequence DNA? I thought it was more like an ethereal chromatography device.
- amelius 6y ago
  It probably just inferred DNA from fenotype.
- ivanbakel 6y ago
  The tricorder can typically do whatever it needs to, but it's normally portrayed as a super-powered radiation (meaning EM, but also Trek's made-up radiations) scanner. That scanning seems to work down to the molecular level, because IIRC it's often used to check for "DNA degradation/mutation/etc", which is a common enough plot point. That implies the ability to take DNA sequences. But this is just another case of a company trying to ride the Trek-tech bandwagon. A real "tricorder", or anything close, would be a massive leap forward in technology, even if it came in the bulky TOS-style boxes.
  - dwighttk 6y ago
    Heck even if it came in a box the size of the full starship Enterprise
nomercy400 6y ago
This is an app for DNA analysis. The DNA sequencer used costs around 1000 usd, and has bluetooth and wifi connectivity. Any chance for an Android app? Or something open so we can create it ourselves, e.g. OpenDNA? Is DNA analysis that complicated once you have the raw data?
- acqq 6y ago
  For those who didn't know, the mentioned "DNA sequencer" device is the smaller one on this page, the bigger already has a display and its biggest dimension matches iPhone X (but it's thicker and wider) so also relatively pocket-size: https://nanoporetech.com/products/minion-comparison https://nanoporetech.com/products/minion-comparison A new flow cell is needed for every run, pricing for them is in the "Price per flow cell" row. https://nanoporetech.com/products/comparison https://nanoporetech.com/products/comparison
- koeng 6y ago
  They’re making the Smidgion which can directly connect to smartphones. The minion needs a USB connection tho, which is the $1000 one. The raw data is actually pretty intense to decode - it took my 4 core i7 processor (2016) about 30 hours to basecall like 3gb of data from a flongle, which normally on minion flow cells you get like 30gb. This can be greatly increased with GPUs, however. Nanopore is very locked down, but data you can share freely.
alextheparrot 6y ago
I still think the Nanopore people just have a tough product to fit into the market. This technology had much higher error rates than traditional sequencing (~15%) and the use cases where I want to analyze something out in the field so badly are not numerous. Collecting samples and sending them to your centralized sequencing facility is going to remain the most cost vs quality effective option. Additionally, sequencing is a huge overkill for a diagnostic test, especially when with the cost and complexity of analysis being so high. Anyone have an idea of a market or research project where this thing is a first-choice tool? Edit: I stand corrected, seems some people are trying to use it in front-line clinical tests with post-analysis accuracy roughly on par with Illumina machines. [0] https://www.nature.com/articles/s41587-019-0156-5 https://www.nature.com/articles/s41587-019-0156-5 [1] https://www.nature.com/articles/s41591-020-1105-z https://www.nature.com/articles/s41591-020-1105-z
- hobofan 6y ago
  Accuracy as you have noticed has been getting better, and keeps improving with their newer iterations, which include e.g. dual read heads in the nanopore. > Anyone have an idea of a market or research project where this thing is a first-choice tool? Plants. They often have huge genomes with sections that are hard to sequence with traditional methods with shorter read lengths.
  - alextheparrot 6y ago
    I think that’s a use-case for Nanopore in general, but they explicitly call out that the app here is only useable against small genomes (Virus/Bacteria). I actually really prefer the movement away from optical reads and using smarter materials, some of the PacBio stuff is still optical but is focused on single cell work mediated by nano-materials as well which is interesting. The part I was really interested in was why portability matters, instead of just having a bench-top Nanopore. I think the idea is that it will be more hobbyist friendly, would be fun to sequence random stuff while hiking. My concern is that the market for these devices isn’t actually that large, as any place doing meaningful analytics is probably going to want a bench top unit. Looking at the prices, now, though I think $1,000 for the minION is about what I’d be willing to pay for that vs a $50,000 benchtop unit. The fact that it does RNA too is huge, as that has a lot of benefits to doing it as close to site of harvest.
LinuxBender 6y ago
Is there an open source program that runs on Linux that works with this device and does not require internet?
- vikramkr 6y ago
  The device is just an oxford nanopore minIon, a commercially available nanopore sequencer
  - LinuxBender 6y ago
    Ah, I see. I found the manual. [1] Thankyou! Windows – 7, 8, 10 OSX – Sierra, High Sierra, Mojave, Catalina Linux – Ubuntu 16.04 or 18.04 [1] - https://community.nanoporetech.com/requirements_documents/minion-it-reqs.pdf https://community.nanoporetech.com/requirements_documents/mi...

43 points by dnetesn 6y ago

I didn't realize that they were this far with Nanopore technology. Really awesome stuff. The weird thing in this article is that they say that "Most of the studying of DNA: aligning, analyzing, is done on large server clusters or high-end laptops." but that an iPhone app can replace that. In my experience, aligning is not computationally intensive at all.

koeng 6y ago
Aligning doesn’t, but basecalling seriously does. The best base callers are still big machine learning models that take quite good GPUs

rapjr9 6y ago

So, can this be used to track where people have been? Follow the plume of DNA from the skin cells they shed? Is it an immediately useful way to tell if someone has COVID-19? Could it be used to covertly build a database with a unique DNA ID for all people? How fast is it, how much does it cost, are there consumables that have to be replaced? Some answers here: https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies https://en.wikipedia.org/wiki/Oxford_Nanopore_Technologies https://nanoporetech.com/ https://nanoporetech.com/ This does not seem to bode well for privacy.

dmos62 6y ago
It's sad that our privacy and hence well-being is so intimately threatened by technological progress. It says something about the powers that be. In the ideal setup, we'd only be thrilled by new technology, while legislature and its enforcement would regulate things that might harm us, like tracking.
amelius 6y ago
> So, can this be used to track where people have been? The same can be said about cameras. And DNA tracks are easier to fake.
koeng 6y ago
Yea, you can use it for COVID19 diagnostic tests. I did that back in April-ish for a project before they redirected the Nanopore reagents to commercial COVID testing. Yes, it could be used to build a database, so long as you have a good amount of DNA from the person. Honestly, governments are already doing this with Illumina runs, so no diff there really. It immediately generates runs, and tapers off at about 12-24 hours, and using a full flow cell takes like 48. How long you run it for depends on depth of reads. Flongle flow cells cost $99 and approximately $200 at end of day and minion flow cells cost about $1000, with minion being about 10x as good as flongle. The primary cost is definitely consumables, the capex for these devices is very low.

helsinkiandrew 6y ago

Not to be picky but did the Star Trek tricorder sequence DNA? I thought it was more like an ethereal chromatography device.

amelius 6y ago
It probably just inferred DNA from fenotype.
ivanbakel 6y ago
The tricorder can typically do whatever it needs to, but it's normally portrayed as a super-powered radiation (meaning EM, but also Trek's made-up radiations) scanner. That scanning seems to work down to the molecular level, because IIRC it's often used to check for "DNA degradation/mutation/etc", which is a common enough plot point. That implies the ability to take DNA sequences. But this is just another case of a company trying to ride the Trek-tech bandwagon. A real "tricorder", or anything close, would be a massive leap forward in technology, even if it came in the bulky TOS-style boxes.
- dwighttk 6y ago
  Heck even if it came in a box the size of the full starship Enterprise

nomercy400 6y ago

This is an app for DNA analysis. The DNA sequencer used costs around 1000 usd, and has bluetooth and wifi connectivity. Any chance for an Android app? Or something open so we can create it ourselves, e.g. OpenDNA? Is DNA analysis that complicated once you have the raw data?

acqq 6y ago
For those who didn't know, the mentioned "DNA sequencer" device is the smaller one on this page, the bigger already has a display and its biggest dimension matches iPhone X (but it's thicker and wider) so also relatively pocket-size: https://nanoporetech.com/products/minion-comparison https://nanoporetech.com/products/minion-comparison A new flow cell is needed for every run, pricing for them is in the "Price per flow cell" row. https://nanoporetech.com/products/comparison https://nanoporetech.com/products/comparison
koeng 6y ago
They’re making the Smidgion which can directly connect to smartphones. The minion needs a USB connection tho, which is the $1000 one. The raw data is actually pretty intense to decode - it took my 4 core i7 processor (2016) about 30 hours to basecall like 3gb of data from a flongle, which normally on minion flow cells you get like 30gb. This can be greatly increased with GPUs, however. Nanopore is very locked down, but data you can share freely.

alextheparrot 6y ago

I still think the Nanopore people just have a tough product to fit into the market. This technology had much higher error rates than traditional sequencing (~15%) and the use cases where I want to analyze something out in the field so badly are not numerous. Collecting samples and sending them to your centralized sequencing facility is going to remain the most cost vs quality effective option. Additionally, sequencing is a huge overkill for a diagnostic test, especially when with the cost and complexity of analysis being so high. Anyone have an idea of a market or research project where this thing is a first-choice tool? Edit: I stand corrected, seems some people are trying to use it in front-line clinical tests with post-analysis accuracy roughly on par with Illumina machines. [0] https://www.nature.com/articles/s41587-019-0156-5 https://www.nature.com/articles/s41587-019-0156-5 [1] https://www.nature.com/articles/s41591-020-1105-z https://www.nature.com/articles/s41591-020-1105-z

hobofan 6y ago
Accuracy as you have noticed has been getting better, and keeps improving with their newer iterations, which include e.g. dual read heads in the nanopore. > Anyone have an idea of a market or research project where this thing is a first-choice tool? Plants. They often have huge genomes with sections that are hard to sequence with traditional methods with shorter read lengths.
- alextheparrot 6y ago
  I think that’s a use-case for Nanopore in general, but they explicitly call out that the app here is only useable against small genomes (Virus/Bacteria). I actually really prefer the movement away from optical reads and using smarter materials, some of the PacBio stuff is still optical but is focused on single cell work mediated by nano-materials as well which is interesting. The part I was really interested in was why portability matters, instead of just having a bench-top Nanopore. I think the idea is that it will be more hobbyist friendly, would be fun to sequence random stuff while hiking. My concern is that the market for these devices isn’t actually that large, as any place doing meaningful analytics is probably going to want a bench top unit. Looking at the prices, now, though I think $1,000 for the minION is about what I’d be willing to pay for that vs a $50,000 benchtop unit. The fact that it does RNA too is huge, as that has a lot of benefits to doing it as close to site of harvest.

LinuxBender 6y ago

Is there an open source program that runs on Linux that works with this device and does not require internet?

vikramkr 6y ago
The device is just an oxford nanopore minIon, a commercially available nanopore sequencer
- LinuxBender 6y ago
  Ah, I see. I found the manual. [1] Thankyou! Windows – 7, 8, 10 OSX – Sierra, High Sierra, Mojave, Catalina Linux – Ubuntu 16.04 or 18.04 [1] - https://community.nanoporetech.com/requirements_documents/minion-it-reqs.pdf https://community.nanoporetech.com/requirements_documents/mi...