Home DNA Sequencing 190
An anonymous reader writes "Wired is running an article about high-tech gifts for Christmas, including a home DNA sequencing kit targeted at kids for under $100. What's next, the Fisher Price Cloning kit?"
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Home DNA Sequencing
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Modding the Airzooka (Score:3, Interesting)
Don't try this at home kids -- try this at someone else's home!
A Toy (Score:4, Interesting)
Obviously it won't have the more dangerous chemicals mentioned previously, and sample purity would be a bit of a joke, but I'm curious as to how well, if at all, this thing would work, and how?
Re:Anyone know how well it actually works? (Score:5, Interesting)
As a biochemist I certainly appreciate the value of the kit in introducting kids to science. Think of it like you'd think of a build-your-own-microscope or build-your-own-electric-motor kit. Yeah, those do make things look bigger and they will turn in a wobbly sort of way, but they aren't useful as real microscopes/motors.
As far as the reference in the article to paternity testing goes - forget it. At the very least you'd have to use a restriction enzyme to generate a fingerprint pattern. This just makes visible the various small chunks of DNA visible which are created from mechanical handling of it.
Most likely you'll get a smear of some sort - not discrete bands like you get from any useful experiment. Also - if you do end up with any patterns you'll probably get a different one any time - hardly a "fingerprint". Then again, the discovery website lists a DNA stain fabricated to look like real DNA in its brief description - so if that is added to the well prior to electrophoresis you could get a pattern of bands - though this would not be from the DNA in your sample.
It is a cute concept though. Your girlfriend will probably appreciate it, although the results will be far inferior to anything she generates at work (assuming she actually works in the lab).
I wish I knew more about the contents of the kit. I'm curious as to what they're using for staining - the gold standard in the lab is ethidium bromide. However, I'm certain that isn't in the kit - it is a very powerful mutagen.
Re:Anyone know how well it actually works? (Score:1, Interesting)
Bag one of these babies and grab some babes DNA, will there be an online database of chick's DNA?
Then we shall bag the Cloning kit next.
Actually that brings up an issue. PRIVACY, what if somebody puts online a database and people start submitting Peoples DNA (from any source).
Distributed Genome Variability Analysis (Score:5, Interesting)
I guess the next frontier is Sequencing@Home with people bragging about how many of their own base pairs or chromosomes they have sequenced.
Re:A Toy (Score:5, Interesting)
You could use this for PCR, and then do many things with it. You could potentially have a "deluxe" version of the kit for $1000 dollars, including:
1. Basic thermocylcer
2. Reagents/Enzyme for PCR
3. Primers for PCR
4. Reagents/Enzyme for restriction digestion
The kit could then be used for (basic, potentially problematic) paternity testing.
Re:Also known as... (Score:5, Interesting)
It doesn't work that way. In order for such results to be admissible in court, a chain of custody of the evidence has to be established. What this basically comes down to is that a medical profesional has to swear an affidavit that they collected the samples, sealed them and ensured that they went to the lab without any possibility of any of the parties in the case being able to tamper with them.
I took a home paternity test last year, which came out negative. If it had been positive, the mother would still have had no legal grounds for getting child support from me. It would have been necessary (from a legal point of view) for a properly supervised test to have been performed.
(Mind you, if he had been my child, I wouldn't have been such an absolute bastard as to turn my back on my responsibilities. The mother herself suggested that we carry out the test. And she is a lawyer.)
Re:Nice 'gift' for christmas (Score:5, Interesting)
Great Leap Forward (Score:2, Interesting)
Actually this remainds me of Chinas "Great Leap Forward [wikipedia.org]" when Mao thought it would be a great idea to have people produce steel in their backyards. Needless to say the little steel produced was useless and lot of time and resources were waisted.
Re:Anyone know how well it actually works? (Score:3, Interesting)
I've RTFA's for almost five years now about DNA sequencing, and how uber-clusters of Linux boxes have been used to help this process (a recent Linux Journal article talked about this). However, never have I seen an explanation of what DNA sequencing really is, and more importantly, what good does having a sequence do? What will we do with this new information? All the articles I see usually have a sidebar with some handwaving about "medical research" and the obligatory "hopefully find new cures for cancer". Usually it just seems to be used by the media and governments as a benchmark to display against the other guys, such as "We sequenced the [animal] gene in 2.37 days, much faster than the [other nationality] team who took three weeks. [our nationality] rules!"
I don't consider myself stupid, but I'm really ignorant about the topic. Can it be explained to a fellow techie in the length of a forum post? As an engineer at heart, I like to know what the final result will be (the "benefit" in the cost/benefit analysis).
Total nucleic acid (Score:2, Interesting)
However, this is a crude extract with no purification or isolation. Fingerprinting this kind of prep is worthless to answer questions other than is there nucleic acids in the sample unless they are including some sort of probe (highly unlikely). Fingerprinting entire genomes of multichromosomal organisms would not be something worth doing (beyond the gee-whiz factor) unless you move into doing blots, or if you worked with entities with single chromosomes such as bacteria or mitochondrial DNA. They include lambda DNA, maybe that let's them do a fingerprint, maybe with a double digest to do some mapping.
Given the fact that it appears that the DNA stain seems to be responsible for the pattern seen- the good news for parents fearful that Jane or Johnny might discover something about her/his parentage, everyone in the world will look like they have identical patterns- unless the kid is smart enough to figure out that it might mean the parents might be a little too closely related.
Re:Total nucleic acid (Score:5, Interesting)
The product site has info on how to get lambda (phage, I assume)DNA to cut & run, which would give you good banding patterns. Heck, I use lambda/HaeIII as my molecular weight marker.
Medical Privacy (Score:2, Interesting)
Patients have the right to limit the scope of their consent, so the woman won her case against the doctor. But no hospital would have placed the burden of blood identification on the immediate family because of related privacy issues. The ruling was that the woman should have had an the blood drawn from herself in advance of the surgery.
I thought that was a very insightful case. Hospitals are probably the last institution that really serve to protect your privacy. They're hardline ideologues on all kinds of things. Hell, the local hospital isn't even allowed to put up any images of Santa because it's a "religious icon." No star-topped Christmas trees either.
Re:It's not DNA sequencing (Score:2, Interesting)
I suspect there are no restriction enzymes. Its extracting total genomic DNA from pea (with options for chicken liver) the DNA will appear as a smear on the gel regardless of digestion. Its probably extracting DNA by ethanol precipitation [exploratorium.edu] looking at the slimey mass of DNA going yuck , then running out a premade DNA ladder (ie mix of DNA of known sizes which would make a much nicer result). Coupled with that there are problems storing the enzymes (I can't think of any that could take prolonged room tempreature storage).
Re:Distributed Genome Variability Analysis (Score:3, Interesting)
The sequencers that are used to sequence genomes these days cost about $100k and require 15 minutes of operator time per day. They can conduct about 100 sequencing operations simultaneously. Each cycle takes probably a few hours at most. Each cycle generates around 600 bases of useful sequence. So one of these machines generates around 360 kilobases of DNA in a day (600 bases x 100 parallel operations x 6 sets of parallel operations per day).
Working manually a grad student using manual pipettes for mixing, and standard gel apparatus could probably do about 100 reactions in an 8-hour day. Maybe 200 if they're good. Those reactions would probably only be good for 300-400 bases (the human factor). The humans would waste far more reagents as well.
Keep in mind that the reactions do consume reagents - that aren't cheap. Actually, the two most common ways of labelling the DNA in sequencing are fluorescent tags (which require a laser to measure) or radioactivity (which cuts the productivity of your runs by 1/4th and of course involves radioisotopes in the same sink you wash your dishes in).
I don't see distributed sequencing working anytime soon. It is cheap on the industrial scale already, and there are big issues keeping it from working in the kitchen.