from the nanopour-is-for-really-tiny-cups-of-coffee dept.
[Ed note: We are experimenting with something new with this story on SoylentNews. The submitter has agreed to answer some of your questions. Please submit one question per comment. The most highly-rated comments will be given to the submitter. We'll post another story later with the replies.
Previous stories on MinION:
The MinION - Genome Sequencing in a Handheld Device
A MARC in the Silicon: Sequencing E. coli with the MinION]
I was invited to be a speaker at the TEDxWellington 2016 conference on 6th March. The theme of the conference was trust. Along with all other speakers and crew, I was trusted not to tell anyone about my role in it until I had finished speaking. Attendees were transported from a meeting place at the National War Memorial to the venue in buses that had been blacked out The conference was the first public event that was held inside Peter Jackson's private cinema at Park Road Post Production in Miramar, Wellington, New Zealand.
Due to an enclosed fabric tunnel, the cinema inside the venue was the first thing that attendees saw after getting into the buses. Only a few people knew the speaker lineup, and speakers for the second and third sessions were distributed throughout the audience, so that attendees couldn't tell who else would be talking.
The talks, prior to post-production and editing are available on a live stream feed. My talk was about DNA sequencing using the Oxford Nanopore MinION and starts at timecode 01:29:00 on the recorded video. A video of my presentation will be edited and uploaded to the TEDx YouTube channel in a few weeks.
Here's a brief point summary of my talk:
[Continues.]
- DNA is everywhere.
- DNA sequencing is the process of converting the physical thing of DNA into a model (most commonly, a sequence of letters).
- Sequencing was used in remote areas of Africa for fast tracking of Ebola virus outbreaks
- Sequencing was also carried out on the slope of a volcano in the rainforests of Tanzania.
- These were only possible thanks to the MinION, a device that is so small that it can be taken almost anywhere.
- I started a sequencing run about 3 minutes before my presentation, and was able to show results (and carry out a basic BLAST search) during the talk.
- DNA sequencing could be used in the future in doctor's clinics to get results before the doctor has finished their consultation.
- I had converted the squiggle data from the MinION into sound, and played a 17s-long sound clip of tomato DNA moving through a nanopore.
- DNA sequencing is more affordable than a plane ticket across the world, and soon will be more affordable than a plane ticket across the country
- People should trust in the disruptive potential of this technology, and get excited about the future applications. That will help me (and other researchers) to make it even better.
It was quite a big challenge filtering my knowledge of sequencing to a point where it could be understood by a few people in a general audience. I am greatly appreciative of all the other speakers for giving me wonderful feedback on the many things that went right over their head.
[Since the time this was submitted, there is a new blog posting about the TEDxWellington event: TEDxWellington 2016 Review | The Story Of Trust. As the submitter put it: "There's quite a lot to take in with that post, but it can mostly be summarised as 'we did a lot of things to try to entertain our attendees by continually surprising them.'" -Ed.]
Related Stories
[Editor's Comment: This article might sound a bit like a soyvertisement but it has been submitted by one of our community and someone who is well qualified in his field - David Eccles from the Malaghan Institute of Medical Research in New Zealand. It is interesting to read about what is considered currently to be state of the art in field genome sequencing.]
On the 14th and 15th of May, 2015, Oxford Nanopore Technologies held their inaugural nanopore sequencing conference, London Calling. The conference was set up to inform people about the current progress of Oxford Nanopore's first sequencing device, the muesli bar-sized, USB-powered MinION. Over 250 people were in attendance at the conference, representing 35 countries, including two from New Zealand: Nicole Moore from Environmental Science and Research, and David Eccles from the Malaghan Insititute of Medical Research. Over the course of two days, these attendees discovered how the MinION is quietly turning the world of sequencing inside out.
Everything needed for sample preparation and sequencing can fit into a single piece of checked luggage on an airplane. The MinION is robust enough to make it across unsealed roads to remote parts of Africa, where it has been used for sequencing on-location during the Ebola outbreak. The MinION has also been put through its paces for tracking the traffic of organisms. Detection at the species level can be achieved in under 20 minutes of sequencing, and very subtle changes for the same species from different origins can be identified in less than an hour.
Clive Brown, Chief Technical Officer for Oxford Nanopore Technologies, gave a brief summary of what is to come in the near future of nanopore sequencing:
- A fast mode for sequencing, allowing a human genome to be sequenced with high reliability in a 2-day run.
- An improved Mk II sequencer, with six time the throughput and six times the run time of the first sequencer.
- A clip-on sample preparation laboratory (Voltrax), allowing preparation and sequencing directly from blood in 20 minutes.
- Time-based pricing, reducing the minimum cost of a single-molecule sequencing run to $50.
- A 48-cell desktop sequencing device (PromethION) that can produce over 6 terabases of sequence per day, making sample preparation time the slowest part of the sequencing process.
I am part of an international team of researchers who have been exploring the capabilities of the MinION Sequencer, the MinION Analysis and Reference Consortium (MARC). Our first paper on this exploration has just been published in f1000 Research. Five separate labs carried out four sequencing runs each of the same strain of E. coli, and a few more labs helped to analyse the results. If you're interested in seeing what this technology is capable of (or at least, what it was capable of about 6 months ago), check out the paper here, or download the data here.
The Oxford Nanopore MinION is a small DNA sequencer that plugs into the USB port of a laptop and sequences DNA by measuring changes in an electric current as the sequence is passed through one of 4096 pores in the sequencing device. These electrical signals are combined into events that describe the movement of a single base, and the events are then base-called to generate DNA sequences.
The MinION sequencer is almost entirely electronic, stripping away everything that makes existing DNA sequencing technologies big, heavy, slow and expensive. This has meant that the MinION is uniquely able to be used in remote areas where other sequencers just can't reach: sequencing Ebola on-site in Africa, sequencing the DNA of small frogs in the Amazon rainforest, and more recently sequencing DNA in NASA's vomit comet.
Previously: The MinION - Genome Sequencing in a Handheld Device
You may recall that I did a TEDxWellington talk about two months ago. My talk was about sequencing on the Oxford Nanopore MinION. The video of this talk has now been edited and is available on the TEDx Youtube Channel.
Although I haven't explicitly said it in the talk, this is a live demonstration of DNA sequencing, and possibly the first such demonstration outside ones done by Oxford Nanopore Technologies. I spend the first half of the talk stalling for time while the initial QC finished, and then a bit of time after data analysis (i.e. a BLAST search) discussing where we could be heading.
To give a bit of an idea of the challenges involved in doing this, all my equipment for sequencing (excluding laptop) was brought to the venue the day before (for the dress rehearsal) in a 30cm polystyrene cube.
On arrival at the venue, I stored the ONT reagents in a freezer in the nearby kitchenette, and prepared the flow cell about half an hour before my talk. In my lab I had prepared two tubes with pre-mixed reagents (one with library + water + running buffer; one with fuel mix), so I was able to use a fine-nozzle pasteur pipette to do the final mixing and loading onto the flow cell.
I had a slightly flakey USB connection on the MinION, so couldn't start the run off-stage (it was very sensitive to bumping). Despite starting the run during the video prior to my talk, I still had a bit less run time than the 5 minutes I had planned for, so had to tweak my presentation a bit to fit the end of the QC step into my talk.
The sequencing run was carried out using a laptop I had purchased for $900 NZD and set up a couple of weeks prior to the conference. Sequencing was done from battery power only, using the WiFi connection because the wired connection was being used for conference live streaming -- this might be the reason why called sequences took a little longer than a couple of minutes to download onto the laptop. The dress rehearsal the day before was the first time I'd carried out a sequencing run on that particular laptop, and made me aware that the screen resolution was less than the recommended minimum requirements from ONT.
Despite everything that happened, I don't think any of the audience were aware that I had any problems with my run (apart from needing to use my dress-rehearsal backup sequences), which aligns very nicely with the themes of trust and secrecy for this year's conference.
For those interested in looking at the actual reads from that run, I've put the "pass" reads into a dropbox folder.
If you want a little low-hanging-fruit programming project to work on, then you can have a look at improving the recently published open source base callers:
- DeepNano (Neural network basecaller): Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads; Vladimír Boža et al., Comenius University
- Nanocall (HMM basecaller): An Open Source Basecaller for Oxford Nanopore Sequencing Data; Matei David et al., Ontario Institute for Cancer Research and University of Toronto
Writing at Space.com, Sarah Lewin describes some of the scientific cargo that tomorrow's Dragon9 launch will carry to the International Space Station:
SpaceX's ninth commercial cargo mission, launching early Monday (July 18), is lugging a selection of strange science to the International Space Station -- living, beating heart cells, microbes from a nuclear disaster, a tiny DNA sequencer and more.
[...] One experiment won't take up a lot of space, but it has the potential to be a huge research boon to the orbiting lab -- the space station's first DNA sequencer, which is about the size of a "fun-size Snickers bar," said Sarah Wallace, a microbiologist at Johnson Space Center (JSC) in Houston.
[...] The astronauts will also be bringing aboard live heart cells, which they will cultivate for one month to test for changes in their sizes, shapes and beating patterns.
[...] Another experiment that investigates bone loss in space will test some technology that could potentially save researchers from sending similar experiments aloft: It will compare changes in bone cells that have been flown to space with ones that got the zero-g experience on Earth, levitated magnetically in a microgravity simulator.
[...] In addition to sending up those heart and bone cells, plus some tomato seeds that will be grown in schools once they return to Earth, the spacecraft is bringing another strange visitor: microbes that emerged after the Chernobyl nuclear reactor, located in Ukraine, melted down catastrophically in 1986.
[...] Researchers are also sending up a demo of a phase-change material heat exchanger, which will test wax-based and water-based substances that can melt and freeze as the temperature outside a spacecraft changes, absorbing excess heat and re-releasing it to keep the craft warm as it orbits in and out of Earth's shadow, going from blazing heat to chilling cold. They're also testing a receiver that will track ships on the ocean, computer processors to stick outside the station and check for radiation-related errors, and a more efficient solar cell.
The photo of the DNA sequencer shows that it really does resemble a "fun-size Snickers bar", though with two layers!
The "DNA sequencer" is made by Oxford Nanopore Technologies and is called MinION about which we have had a few stories posted here.
Related:
SpaceX Set to Launch 9th Dragon CRS Mission 12:45am EDT (04:45am UTC) on July 18
(Score: 2) by takyon on Monday March 14 2016, @12:05PM
The Nanopore website [nanoporetech.com] mentions connecting to a PC or laptop using a USB port. How about a smartphone? What software is used on the PC/laptop/phone to receive data?
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by takyon on Monday March 14 2016, @12:10PM
When/where/how should the sequenced genome be compressed [wikipedia.org]? Does the MinION dump the raw data to a PC, which will then compress it?
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by takyon on Monday March 14 2016, @12:20PM
Where do you acquire the graphene for nanopores (assuming that is what it used [nanoporetech.com] in current generations of the MinION), and have the costs fallen?
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by takyon on Monday March 14 2016, @12:26PM
Is Oxford Nanopore Technologies involved with the 100,000 Genomes Project [wikipedia.org] or any other emerging population-scale sequencing efforts?
http://blog.illumina.com/blog/illumina/2014/01/14/the-power-and-promise-of-population-scale-genomics [illumina.com]
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 2) by takyon on Monday March 14 2016, @12:30PM
How are competing sequencing products better or worse than MinION, on factors other than portability/lack of portability?
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 0) by Anonymous Coward on Monday March 14 2016, @03:10PM
I will try to answer some of your questions while waiting for gringer to show up. To be clear, I have not used the MinION platform.
--I am not aware of anyone attaching the sequencer to phone so far. I suspect it may not be that difficult given how the software part operates. Most of the processing and analysis currently happens on the company's cloud. Metrichor is the name of the software/company from OxfordNanopore. However, efforts are on to make it run local by may researchers and the company itself is open sourcing the software. Besides they are changing the way they process the squiggles from HMM to neural networks and call the squiggles themselves rat5her than converting them to base-pairs. This is so computation can become less intense, but that is in the next version.
--The genome/sequence is probably compressed in cloud by metrichor. MinION does not dump the raw data to the PC but takes it to cloud. Metrichor converts the electrical squiggles to base-paris and displays results in real time. The computational requirements for this part is rather beefy and cant be done a phone - as yet.
--Current generation pores are protein pores. Graphene pores are probably in the future.
--I dont think MinION is being used in the population scale sequencing projects currently underway.
--This technology allows to sequence long stretches of DNA which is a much sought after quality. That is an advantage for many researchers, more so than the portability. Among the current technologies PacBio has a similar capability. However it costs a lot (~$500K??) and needs rather hefty housing requirements and is certainly not portable. However it is a proven technology, error rates are low and random in it and lot of publications have come out of it. MinION has ways to go but I hope it will get there soon.
Some parts of the answer may be not clear but I am looking from inside so cant see it. I will try to clarify if needed. Hope this helps. Cheers,
(Score: 2, Disagree) by sbgen on Monday March 14 2016, @03:29PM
Looks like I forgot to click something last time so reposting it:
=================================================
I will try to answer some of your questions while waiting for gringer to show up. To be clear, I have not used the MinION platform.
--I am not aware of anyone attaching the sequencer to phone so far. I suspect it may not be that difficult given how the software part operates. Most of the processing and analysis currently happens on the company's cloud. Metrichor is the name of the software/company from OxfordNanopore. However, efforts are on to make it run local by may researchers and the company itself is open sourcing the software. Besides they are changing the way they process the squiggles from HMM to neural networks and call the squiggles themselves rat5her than converting them to base-pairs. This is so computation can become less intense, but that is in the next version.
--The genome/sequence is probably compressed in cloud by metrichor. MinION does not dump the raw data to the PC but takes it to cloud. Metrichor converts the electrical squiggles to base-paris and displays results in real time. The computational requirements for this part is rather beefy and cant be done a phone - as yet.
--Current generation pores are protein pores. Graphene pores are probably in the future.
--I dont think MinION is being used in the population scale sequencing projects currently underway.
--This technology allows to sequence long stretches of DNA which is a much sought after quality. That is an advantage for many researchers, more so than the portability. Among the current technologies PacBio has a similar capability. However it costs a lot (~$500K??) and needs rather hefty housing requirements and is certainly not portable. However it is a proven technology, error rates are low and random in it and lot of publications have come out of it. MinION has ways to go but I hope it will get there soon.
Some parts of the answer may be not clear but I am looking from inside so cant see it. I will try to clarify if needed. Hope this helps. Cheers,
Warning: Not a computer expert, but got to use it. Yes, my kind does exist.
(Score: 2) by takyon on Monday March 14 2016, @08:23PM
I appreciate it, thanks.
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 3, Informative) by gringer on Monday March 14 2016, @10:19PM
Among the current technologies PacBio has a similar capability. However it costs a lot (~$500K??) and needs rather hefty housing requirements and is certainly not portable. However it is a proven technology, error rates are low and random in it and lot of publications have come out of it.
I'm trying to wait for the "official" list of questions, but feel that I need to respond to this point now.
Both PacBio and ONT are producing sequencers that produce long reads off single molecules, but the technology and approach of sequencing is very different. In other words, while the output is [currently] similar, the way you get there is different.
The biggest difference, from my point of view, is that PacBio sequencers carry out sequencing by synthesis, while ONT sequencers (e.g. the MinION) carry out sequencing by observation. This has two fairly big advantages:
We don't yet know how to properly use the output from the MinION, but a basecaller has been created by ONT to convert signal output into a base sequence. The assumed models are all in software (in the base-caller), and that can be updated and improved later in-silico.
Considering purely what is useful right now, Sequel is a bit cheaper per run ($700 vs $1200) for about five times the theoretical maximum yield (10 Gb vs 2 Gb), as long as you ignore the cost of purchasing (and maintaining) a Sequel.
Ask me about Sequencing DNA in front of Linus Torvalds [youtube.com]
(Score: 2) by takyon on Monday March 14 2016, @08:34PM
What achievement is the company using to immediately promote the MinION? For example, are you or partners going out into the field and rapidly sequencing undiscovered bacteria, a certain taxonomical group of plants/animals/fungi, or an endangered population of big cats to preserve genetic diversity?
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]
(Score: 4, Interesting) by martyb on Monday March 14 2016, @12:19PM
There has been much discussion on this site about the-powers-that-be vacuuming up all the information that they can. Not just from government entities (such as the NSA and GCHQ), but also corporate entities, as well (data brokers, insurance companies, Google, etc.)
I have a two-part question:
A.) What do you see as the greatest opportunities in the use of a tool such as MinION?
B.) How can we protect ourselves from having that information used against us?
Wit is intellect, dancing.
(Score: 0) by Anonymous Coward on Monday March 14 2016, @04:56PM
How can we protect ourselves from having that information used against us?
YOU DON'T! You should just trust us, goy.
(Score: 2) by wonkey_monkey on Monday March 14 2016, @12:39PM
Sequencing that Stimulates the Sensors
Sufferin' succotash!
I was invited to be a speaker at the TEDxWellington 2016 conference on 6th March. The theme of the conference was trust.
Unfortunately I was deliberately given the wrong address, thus learning a valuable lesson on the subject.
systemd is Roko's Basilisk
(Score: 0) by Anonymous Coward on Monday March 14 2016, @12:55PM
We drove you from canada to new zealand in a bus, trust us.
(Score: 2) by shrewdsheep on Monday March 14 2016, @01:32PM
To expand on your second point:
DNA sequencing is more affordable than a plane ticket across the world, and soon will be more affordable than a plane ticket across the country
Which is way too expensive to use in medical practice. How can I trust somebody trying to misinform me?
People should trust in the disruptive potential of this technology, and get excited about the future applications. That will help me (and other researchers) to make it even better.
Any new technology has a disruptive potential. If you imply that this should make me feel excited about the future applications unconditionally, again I feel mistrust. This question is orthogonal to the technology itself, in principal, and sometimes it is better to talk about either aspect instead of both (did the other speakers point this out?). To the point, next generation sequencing technologies harbor great dangers besides the potentials.
(Score: 2) by wonkey_monkey on Monday March 14 2016, @04:25PM
Which is way too expensive to use in medical practice.
Or too cheap! Depends how you ultimately pay for your healthcare, I think...
Any new technology has a disruptive potential. If you imply that this should make me feel excited about the future applications unconditionally, again I feel mistrust.
Agreed. Transformative should be the thing to highlight. Things can be transformative without being disruptive, and vice versa.
systemd is Roko's Basilisk
(Score: 0) by Anonymous Coward on Monday March 14 2016, @01:32PM
Rather confusing. Is there any relationship between trust/secrecy and the talk topic?
(Score: 2) by darkfeline on Monday March 14 2016, @02:31PM
Trust that this technology won't be abused to abuse your privacy.
Join the SDF Public Access UNIX System today!
(Score: 3, Interesting) by bitstream on Monday March 14 2016, @01:35PM
Is there any hindrance to provide software with the hardware that runs on the free Unixes like FreeBSD and Linux?
(Score: 2) by VLM on Monday March 14 2016, @03:26PM
Comment on the search and replace job done below:
DNA sequencing could be used in the future in employment interviews to get results before the applicant has finished their interview.
(Score: 2) by VLM on Monday March 14 2016, @03:28PM
How do you handle the HIPPA problems of the volume of data?
I guess to expand on what I'm talking about, its one thing to "lock down" and "keep secret" my O+ blood type (err, I think thats what it is, anyway). How do you handle "large amounts" of genetic data?
(Score: 1) by anubi on Tuesday March 15 2016, @07:42AM
For what reason should having an O+ blood type be kept secret?
Universal donor and some rich man, if he needs more than you can spare, can just bribe the blood-taker to take it all while you are on the donation bench?
"Prove all things; hold fast that which is good." [KJV: I Thessalonians 5:21]
(Score: 2) by Fnord666 on Tuesday March 15 2016, @10:41AM
Oneg is the universal donor.
(Score: 4, Interesting) by VLM on Monday March 14 2016, @03:32PM
Is this gadget useful for testing of the food supply? I'm not talking about paranoid GMO stuff, but is it reasonably sensitive such that you could grind up wheat into flour, mix thoroughly, and test for bug DNA to verify bug contamination of the original wheat? Most of the stuff in the flour would be gluten protein and "wheat parts" but could you search for bug DNA specifically instead?
(Score: 2, Interesting) by sbgen on Monday March 14 2016, @03:57PM
--Yes. OxfordNanopore has designed a specific application they call WIMP (What is in my pot). It sequences the DNA and simultaneously matches it against database (pre-cured/computed/compiled) containing information from various microbes to identify which one is in the test sample. I imagine you can place the sequence information from whatever you are interested to test for in that database and go to town with the your sample. You should get some broad answers within 15 minutes or so - according to the information available online.
Cheers
Warning: Not a computer expert, but got to use it. Yes, my kind does exist.
(Score: 0) by Anonymous Coward on Monday March 14 2016, @10:33PM
What are your feelings on the current unreliability of polymorphisms at producing meaningful health outcomes? Besides obvious hereditary diseases and tumor profiling, there doesn't really seem to be much predictive power of having a genome sequence for a patient.
(Score: 0) by Anonymous Coward on Monday March 14 2016, @10:38PM
How well does MinION handle regions that are prone to sequencing errors like those mentioned in the linked paper:
http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0269-0 [biomedcentral.com]
(Score: 1) by devlux on Monday March 14 2016, @11:54PM
I worked in a lab for years. Paid for part of my college that way.
Contamination and cross contamination of samples is always A HUGE problem.
I see nothing here that addresses demunging of results or even that there is an attempt.
Consider a sample taken in a hotel room. Even after cleaning, there are literally thousands of people's skin & hair flakes laying about all over the room.
There is no way to distinguish one from another and it's unlikely that normal room swabbing would be able to distinguish one person from another.
So how does this system purport to differentiate or at least make some control against contamination?
(Score: 2) by takyon on Tuesday March 15 2016, @03:23AM
I would have to assume it sequences everything it comes across, then ranks by frequency.
[SIG] 10/28/2017: Soylent Upgrade v14 [soylentnews.org]