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Pocket-Sized DNA Reader Used To Scan Entire Human Genome Sequence (arstechnica.com)
An anonymous reader quotes a report from Ars Technica: A few years back, a company called Oxford Nanopore announced it was developing a radically different way of sequencing DNA. Its approach involved taking single strands of the double helix and stuffing them through a protein pore. With a small bit of current flowing across the pore, the four bases of DNA each created a distinct (if tiny) change in the voltage as it passed through. These could be used to read the DNA one base at a time as it wiggled through the pore. After several years of slow progress, Oxford Nanopore announced that its sequencing hardware would be as distinctive as its wetware: a USB device that could fit comfortably in a person's hand. As the first devices went out to users, it became clear that the device had some pros and cons. On the plus side, the device was quick and could be used without requiring a large facility to support it. It could also read very long stretches of DNA at once. But the downside was significant: it made lots of mistakes.
With a few years of experience, people are now starting to learn to make the most of the devices, as demonstrated by a new paper in which researchers use it to help sequence a human genome. By using the machine's long reads -- in one case, nearly 900,000 bases from one DNA molecule -- the authors were able to get data out of areas of the human genome that resisted characterization before. And they were able to distinguish between the two sets of chromosomes (one from mom, one from dad) and locate areas of epigenetic control in many areas of the genome. In light of all the distinct information it can provide, the machine's error rate is seeming like less of a problem.
With a few years of experience, people are now starting to learn to make the most of the devices, as demonstrated by a new paper in which researchers use it to help sequence a human genome. By using the machine's long reads -- in one case, nearly 900,000 bases from one DNA molecule -- the authors were able to get data out of areas of the human genome that resisted characterization before. And they were able to distinguish between the two sets of chromosomes (one from mom, one from dad) and locate areas of epigenetic control in many areas of the genome. In light of all the distinct information it can provide, the machine's error rate is seeming like less of a problem.
Just remember it was a cautionary tale and NOT an operations manual.
Just do multiple passes and match the commonalities. Should be an easy way to sort out the errors and make it much more accurate
in finding out what kinds of DNA is in my pocket,
"Resisted characterization" and yet people know if there are errors there or not.
Just need to ID marker DNA sequences not the whole thing.
Scanning for Flu. Searching for H1N1, Negative, H1N2 Negative........... H2N3 POSITIVE! Confirmation Scan? Y/N?
... and it (kinda) works as advertised. It is also VERY low cost (compared to the previous generation of sequencing machines which cost 700K and up, it costs about $1K). The main disadvantages are that 1) it's still inaccurate, maybe only in the ~90% accuracy rate (not a good thing when you're reading 3B base pairs) and 2) the reagents and flow cell used are expensive (so on big jobs you're almost better off using a traditional sequencer). Still, it does do LONG reads which gets over one of the big disadvantages of the previous gen. machines.
Even with a high error rate, if the errors are UNBIASED then you can overcome them by simply sequencing the same area over and over again to come up with a consensus. This is called "coverage" and usually a factor of 10X is used but if the sequencing technology is cheap enough why not do it 30X or 100X or more?
For us citizen scientists, you'll still need a way of processing and purifying your DNA, I'm trying to get a Bento Lab (hopefully shipping in a month or two). Also the technology will hopefully get better and better, the next version will supposedly have the nanopore membrane separate from the flow cell so the whole thing won't have to be replaced when the membrane is used up. (The version after THAT supposedly will a tiny device directly attachable to an iPhone with an even tinier replaceable membrane so maybe it'll become really cheap to sequence DNA; at parties even :). Finally, I think they may be moving to freeze dried or otherwise non-perishable reagents so the storage requirements will become a little easier (I have a dedicated battery backed freezer at home).
Now with CRISPR kits for only $40, there's no end to the fun (and disasters) that we can do with our basement genetic experiments!
I should mention you'll need a little lab experience and know how to use a pipette and have steady hands! Go take some courses at the local community college and you'll be good to go. (Of course in order to interpret your results you'll need to study BioInformatics, my specialty :)
Something tells me you won't be scanning a lot of vagina, scientifically or otherwise
no one gets convicted of a crime based on one of these things.
Cuz traps are gay.
I did a Q&A on this sequencer on SoylentNews a couple of years ago:
https://soylentnews.org/articl...
The technology has improved substantially since then. Feel free to ask me any more questions about the sequencing. Although I'm not an author on this paper, I'm fairly familiar with the sequencing project that was done, and am happy to answer any general questions you might have on this technology.
Ask me about repetitive DNA
Slashdot trolls in 2017 are fucking lame. Come on man put some effort into it. This is not /b/, itâ(TM)s Slashdot and our trolls traditionally put effort into their work
Excuse the Unicode crap in my posts. That's an apostrophe, and slashdot is busted.
Employers will use such under the table to screen candidates for medical and/or genetic problems. I've worked for slimebags who would happily cheat at anything to gain an edge.
Table-ized A.I.
>in_my_day_trolling_meant_something.jpg
This reminds me of the Human Genome Project. After a few years of trying to get funding for a fifteen year project to sequence the entire human genome, the Reagan administration allocated $3 billion to get started. It was "finished" 13 years later. Now this iPhone doohickey does it in seconds or minutes.
They're even worse this year:)
Fair point!
Excuse the Unicode crap in my posts. That's an apostrophe, and slashdot is busted.
Allow me to be the first to wish you a happy New year:)
Cheers!
bring on the DNA-reader PAM module so I can log into my laptop by licking instead of swiping my finger. on second thoughts, maybe not a good idea because everyone can get a spit sample and log into my linux...
Your heart is true, you're a pal and a cosmonaut. -PCP
Nanopore is more accurate when matching sequences at the signal/electrical level, but almost no one is doing that yet.
Reminds me matching peptide sequences at the mass-spectrometry level in proteomics (Disclaimer: used to work at GeneBio).
"Sufficiently advanced satire is indistinguishable from reality." - [Tips: 1DrYakQDKCQ6y52z6QbnkxHXAocMZJE61o ]
There are two plagues in current WGS: errors in sequence: frameshifts on monomer runs, flaky stop codons in the middle of ORFs etc, and problem of assmbly of short reads in repeated sequences.
This method helps the second problem.
Errors in sequence can be minimized by doing things several times.
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.
The correct response: "Use it to scan OP's mouth."
Someone mentioned 454?
To the best of my knowledge, 454 was a small company on the East Coast, maybe New Hampshire? They were acquired by Roche; the whole operation was moved west.
Did I say the whole operation? Well, they picked and chose who they wanted and who they didn't. In the case of the IT department, they brought exactly one guy west, and, I infer, laid off everyone else.
I came in as a contractor - I gathered the impression that part of the deal involved a two-week-long, all-expenses-paid vacation in Hawaii for the brand new IT manager of the brand new Roche Molecular Systems business unit, staffed with former employees of 454, and I was employed by Roche, on a six month contract, starting by covering for the IT manager while he took his two-week-long vacation.
It was during this period that the manufacturer of the pocket-sized DNA sequencer announced their new product.
I tried to discuss this new product with some of the people I was working with but they were uninterested and/or hostile towards the concept. In retrospect, this makes more sense once you realize that Roche manufactures huge DNA sequencing machines the size of a desk, and that the new equipment rendered their six-figure hardware as obsolete as dinosaurs.
The week after the IT manager came back from his vacation he terminated my six-month-long contract. In retrospect I do not believe that Roche intended to employ me for six months, and I believe that they entered the contract in bad faith.
I think one of the things he was angry at me about was that one of the 454/Roche researchers had asked me why 23 of the 24 CPUs in her team's Linux boxes were idle, and I had replied - drawing upon my three decades of experience with parallel processing R&D - with a brief tutorial on sequential versus parallel processing, including URLs to tutorials, Wikipedia pages and Python libraries. I pointed out the command-line utilities available under CentOS for binding processes to specific cores, and the utilities available for measuring performance (uptime(1), for instance, quite properly displays a line for each of the 24 CPU cores). I explained that software had to be written differently in order to run in parallel. I introduced her to the concept of 'threads'. All part of my job, I thought.
I later discovered there was some sort of history here of conflict between the researcher(s) and 454, going all the way back to the East Coast, perhaps. The researchers had attempted to install their own instance of Nagios so that they could measure performance - perhaps because they did not feel that they were getting good or useful information from their IT support personnel - and the IT manager who I was filling in for, had DELETED their entire Nagios installation.
I felt really sorry for the researchers. They were just scientists, trying to get hard numbers, and here was IT, not being helpful, but being POLITICAL - "That's MY job!" - and actually DESTRUCTIVE. It boggled my mind.
I've played all of the roles in these sorts of dramas. I've been the guy laid off. I've been the guy who stayed. I've been the guy who boxed it up and shipped it. I've been the guy who received the shipments of equipment, unpacked them and re-installed everything.
The one role I've never played is the Judas who betrays my peer IT employees. I don't do well in environments where I have to withhold information from the people I work with. I've always done better in collaborative environments.
Nor have I ever destroyed Nagios installations. I would be THRILLED to have a PhD who wanted to know more about the IT side of things. Such a person would be more willing to return the favor and share information from their side of the fence. We would both benefit as a result; and so would the company we worked for.
It's too bad Roche wasn't the collaborative, R&D-oriented environment I thought it would be. I miss those days.
Just sayan'.
Wont have to ship samples to first world countries
I would greatly consider paying the $1000 fee for the MinION, if it would save me $10,000+ in specialist fees and gas for diagnosing my daughters possible illness/disease. We've been told by numerous other specialists that we need to be seen by a geneticist to see if she has any genetic disorders causing her symptoms. Which we would gladly do, if her insurance would stop denying the referrals and pay for the testing.
If it was a simple way of finding out if you/someone had the genetic markers for certain inherited illnesses, I would gladly forego the migraines of dealing with insurance and purchase the MinION and provide my daughter's pediatrician with the results.
So, my question is.. is this possible with this device? If so, how hard is it to use to look for these markers, and how reliable is it. If it's as low as 80% accurate, I would still consider it, if I could decypher what I was looking at.