Slashdot Mirror
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 do multiple passes and match the commonalities. Should be an easy way to sort out the errors and make it much more accurate
Just remember it was a cautionary tale and NOT an operations manual.
Don't be ridiculous! I mean, everyone knows that 1984 is the real instruction manual. ;)
Anons need not reply. Questions end with a question mark.
in finding out what kinds of DNA is in my pocket,
... 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 :)
Direct RNA sequencing can be done with the MinION as well, no hardware change needed:
https://store.nanoporetech.com...
Depending on how important it is to sequence all RNA, polyadenylation prior to sequencing might also be needed.
Ask me about repetitive DNA
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.