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?"
You can be replaced by this computer.
Fisher Price Cloning (Score:5, Funny)
Man, I hope not: those Fisher Price kids are genetic disasters. Most of them are bald, have some type of head enlarging disorder, as well as lack of arms and legs. I've even seen one with a pan on his head.
Now Weebles: there's your evolutionary high road...
Re:Fisher Price Cloning (Score:3, Funny)
Re:Fisher Price Cloning (Score:2)
Re:Fisher Price Cloning (Score:3, Funny)
Re:Fisher Price Cloning (Score:3, Funny)
Man, I hope not: those Fisher Price kids are genetic disasters. Most of them are bald, have some type of head enlarging disorder, as well as lack of arms and legs. I've even seen one with a pan on his head.
Now Weebles: there's your evolutionary high road...
Kid takes sample of dad's DNA...
Kid takes sample of mom's DNA...
Kid takes sample of their own DNA...
Sequences them all one by one...
Goes up to mom and dad, points finger...
"YOU'RE NOT MY REAL FATHER!"
Hil
Anyone know how well it actually works? (Score:3, Insightful)
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:4, Informative)
Cyber Green? I think that's fairly safe.... Ethidium Bromide would be bad!
Would have been nice if they could have included some cheap and robust restriction enzyme, to produce fingerprints. However this would then require hybridisation with a probe to bring out a few bands - way too complex/expensive. Anyone think of a cheaper and easier way of producing a nice fingerprint? It would be good to have a Mark II kit that actually did something usefull...
Re:Anyone know how well it actually works? (Score:4, Informative)
And I'm pretty sure it intercolates as well (it only interacts with dsDNA), so it's a potential mutagen. Not proven, but still not up for handing out to kids.
I was just showing that to a labmate, and we think that it could simply be hemotoxylin (sp? I never write it out..as in H&E). It's purple, and since the gel should be fairly devoid of protein, it should specifically stain DNA.
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 fi
Re:Anyone know how well it actually works? (Score:5, Informative)
Well, it's a fair question, and to some degree it's difficult to answer, because ... well, at this point, a lot of DNA sequence information is kind of like Bernoulli's law before airplanes, or the rules of Boolean algebra before computers. IOW, we know that there's a lot we can do with the information, but we haven't actually built the machines yet.
That being said, there's a lot of useful work going on with at least some DNA sequence information right now. Here (as a comp. bio. grad student) are the ones I can think of at the moment:
Re:Anyone know how well it actually works? (Score:2)
Re:Anyone know how well it actually works? (Score:2)
Re:Anyone know how well it actually works? (Score:5, Informative)
1. Obtain a pure sample of DNA to sequence. You have to know a little bit of the sequence at the start (not a problem - when you sequence an unknown DNA sample you usually chop it up into bite-sized chunks and insert them into bits of bacterial DNA to make lots of copies of them - this means the unknown DNA has bacterial DNA on either end of it and you already know the sequence of that part).
2. Make a short strand of DNA that binds to the known portion of DNA sequence at the start of unknown portion. These are called primers.
3. Mix the DNA to be sequenced with the primers, heat them up and cool them. This results in long pieces of uknown DNA with the primers stuck to the beginning.
4. Throw in the building blocks of DNA - but a small portion of them are essentially defective and marked with fluorescent tags.
5. Throw in DNA replicating enzymes - these guys look for primers and try to copy the unknown DNA starting at the side of the DNA with the primers attached.
The DNA replicating enzymes will copy the DNA until they accidentally grab a building-block which is defective (which happens a small portion of the time - since most of the building blocks in the mixture work fine). At that point the defective building block is attached to the end of the DNA strand and that strand cannot be copied further.
At the end you end up with a mix of DNA strands that look like:
1. Only one step of the DNA ladder copied - because the first block grabbed was defective.
2. Only two steps copied - the second block was defective.
3. Three blocks copied.
N. The whole strand is copied.
Each of these DNA strands is one step longer than the strand before it. Each has a fluorescent tag at the end - since each ends with a defective block.
You then put this mix of partial strands onto a gel and apply an electrical current - the bigger strands move through the gel more slowly (they get stuck in the pores in the gel).
You end up with a gel with a long ladder-like series of bands - each band is a DNA strand one step longer than the band before it. Each is fluorescently tagged.
Now here is the magic - back when you put the defective building blocks in you actually used a mixture of four blocks (the four types of steps in DNA) each with a different color tag on it. So each band is a different color - corresponding to the color of the last step that was added to the chain. The pattern of colors corresponds to the sequence of the DNA.
I tried to simplify this explanation for those with only a basic understanding of biochemistry. There are various ways of doing DNA sequencing, and these days much of it is automated.
Oh - where the computers come in is this:
A gel like the one I described can only handle pieces of DNA up to about 400 steps long. That means that you can only sequence 400 bases at a time (a base is a step in the DNA ladder). A human being has 4 billion bases in their DNA.
The way you sequence the whole human genome is to chop it up into lots of 400 base units. You actually take lots of copies of the human genome and chop it into lots of random pieces. Then you sequence pieces until you're sequenced about 40 billion bases. Then you have a computer run through the sequences looking for overlaps. The computer will find lots of regions that are sequenced several times, and some regions that weren't sequenced at all. However, it will give you a pretty good sequence of the overall genome, and then some careful followup work can fill in the gaps (the followup work is less easily automated, so they try to get most of it using the random method).
Total nucleic acid (Score:2, Interesting)
However, this is a crude extract with no purification or isolation. Fingerprinting this kind of pre
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.
Re:Total nucleic acid (Score:2)
I agree on the SYBR dangers. In another post [slashdot.org] I postulated that they were using hemotoxylin. No uv needed, and it's non-mutagenic. It's nonspecific, and messy as hell, but who cares about that in this context?
Re:Total nucleic acid (Score:2)
Re:Anyone know how well it actually works? (Score:2)
Heh, doesn't this defeate the purpose of using it for DNA, if it changes the DNA in the process?
Re:Anyone know how well it actually works? (Score:2)
The problem is that when a DNA replication enzyme shows up when the cell needs to divide, it has trouble reading the DNA because of all the dye molecules stuck to the DNA.
So it is only a problem if you want to copy the DNA. Generally you just stain it to get it to show up on a gel, and then you take a photo and toss the whole thing in the trash.
If
Re:Anyone know how well it actually works? (Score:2)
Why not buy it and try it yourself!
http://shopping.discovery.com/stores/s
Buy now, and get it for Christmas! You can use the coupon SHOP10 to get $10 off on all your shopping at the Discovery Store.
Yes, I work for Discovery.
For Free? (Score:5, Informative)
Re:For Free? (Score:2, Informative)
Re:For Free? (Score:2)
Re:For Free? (Score:2)
Nice 'gift' for christmas (Score:5, Funny)
I think a lot of kids wil be very happy with this information.
Re:Nice 'gift' for christmas (Score:5, Funny)
Re:Nice 'gift' for christmas (Score:2)
Definately not nitroglycerine, that's for sure.
Re:Nice 'gift' for christmas (Score:2)
Re:Nice 'gift' for christmas (Score:5, Interesting)
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 relat
How do you do it? (Score:3)
My plan (Score:2)
When my wife and I have kids, we're planning to get the children and ourselves DNA fingerprinted and put the images together in a picture frame for comparison.
Of course, I have no idea how accessible such services are, how expensive, or even what the process is called... still I think it'll look neat on the wall.
Does she know this? (Score:2)
Re:Does she know this? (Score:2)
Of course she knows this!
Besides, women aren't stupid or ignorant - they can always insist that the 'other man' wear a condom. Just because you're the father of the child doesn't mean you're the only one having sex with the mother!
Re:Nice 'gift' for christmas (Score:2)
My first thought was, "Great, now how can I rig this up into a quick viral infection test?"
Imagine the social impacts of a 5-minute, DNA-based 'home STD test', that was as reliable as those 'home pregnancy tests' you get at the supermarket. Find a hottie at the bar, go home, prick your fingers, compare bands and you're good for a wild night of bareback.
It'd be the 70's all over again.
Re:Nice 'gift' for christmas (Score:2)
Anyway the company that makes it is called OraSure [orasure.com]. I believe it is pretty expensive, but the accuracy is supposed to be pretty high.
Re:Nice 'gift' for christmas (Score:2)
Great Idea ... (Score:3, Funny)
Chucky doll? (Score:3, Funny)
Mommy's Little Mouthpiece Teddy Ruxpin goes wireless. Plug Wabi's transmitter into a phone jack, call a designated toll-free number, and record a message. At selected intervals, the transmitter collects the data and sends it to the ursine bot's receiver over a 900-MHz signal. The bear giggles when it gets a message, and your kid simply presses its badge to play the audio. "Hi, Billy! Mommy and Daddy don't love you anymore. I'm in charge now, and things are going to change around this house, dammit!"
Great. Now we can give them Chucky Doll for present.
If only i had something like that when my little sister annoyed me.
Re:Chucky doll? (Score:2)
Of course, I would probably use it by locking the "play" switch on and tormenting some kid, yeah.
Modding the Airzooka (Score:3, Interesting)
Don't try this at home kids -- try this at someone else's home!
Re:Modding the Airzooka (Score:5, Informative)
Re:Modding the Airzooka (Score:2, Insightful)
Re:Modding the Airzooka (Score:2)
Messy? (Score:5, Insightful)
Re:Messy? (Score:2)
Boring ! (Score:4, Insightful)
But, hey, I would like to play with them Pixel Blocks myself [pixelblocks.com] ! (from the same wired review).
Re:Boring ! (Score:2)
"Dad, check this out! I extracted some blood from a mosquito encased in amber and added it to some frog eggs that I found...Hey, they hatched!!! Where did my little baby go?"
ROARRRRRR
Re:Boring ! (Score:2)
Re:Boring ! (Score:2)
Most scientific experiments are boring until you understand the underlying principles. If you drop two balls of different weights from a tower, would they hit the ground at the same time? If you don't understand the point of the experiment, then you're just dropping balls from a building
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: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:A Toy (Score:2)
The kit could then be used for (basic, potentially problematic) paternity testing.
As I'm sure you realize, there are other issues besides the science--unless you can interpret the results as easily as on an EPT test, you'll get more lawsuits than'll be worthwhile.
Re:A Toy (Score:2)
Which is... what?
You could use this for PCR
Which is... what?
Re:A Toy (Score:2)
It will tell you if you have DNA but not much else (Score:2, Informative)
It's not DNA sequencing (Score:5, Informative)
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
Re:It's not DNA sequencing (Score:2)
Actually, this technique is still the primary one used today, I believe. PCR is used to prep samples for RFLP, bt sequencing isn't generally used where it could become evidence in a court case (lawsuit or criminal).
The reason is that courts are all about precedence. Nobody wants to be the prosecution going into a case with a "brand new technique" that the defence will t
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.
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 prod
Re:Great Leap Forward (Score:2)
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
Re:Distributed Genome Variability Analysis (Score:2)
So if the letters on the page of a book are the "sequence", a book would be a gene, a library a chromosome, and all the branches of a library in a large city would be a genome. What this kit does is compare the number of libraries and their relative sizes in two or more big cities (say L.A. and N.Y.C.). It doesn't even com
home DNA test kits: bring 'em on (Score:3, Insightful)
This is a great way to show kids how DNA tests work. I'm all for anything that would help de-mystify DNA testing in the minds of the public. It's particularly gratifying to see that they'll discover it's ultimately a human being making a judgement call about what he or she sees with a microscope.
Re:home DNA test kits: bring 'em on (Score:2)
No microscopes are involved in DNA testing, despite what you may have seen on CSI:Miami.
Then how's the comparison made?
Somehow they have to magnify the images of 2 DNA samples that are to be compared.
Re:home DNA test kits: bring 'em on (Score:3, Informative)
good (Score:4, Funny)
Now all I need is the gene for big breasts, blond hair and low standards, and I might end up with the perfect wife after all.
No not Fisher Price... (Score:2)
No not Fisher Price... Fisher priced [fisherscientific.com].
Sci-fi predicts reality (Score:2, Funny)
Next comes the ejection-bed alarm system!
It's not sequencing, not even real DNA viewing! (Score:5, Informative)
Re:It's not sequencing, not even real DNA viewing! (Score:3, Informative)
It does appear to be 'simulated' which is unfortunate but understandable. DNA stain is extremely carcinogenic. Since it must bind to DNA to work, there's no way to avoid that.
Of course, they could do a better job of making it clear that the results are simulated.
Re:It's not sequencing, not even real DNA viewing! (Score:2)
~GoRK
I'll wait for Genester (Score:5, Funny)
You have to be careful however. Last night I downloaded and cloned Madonna, but she just stood there screaming "What the hell do you think you're doing?". It turns out that companies post fake DNA to flood the network. Bummer! It was such a pain disassembling the clone afterwards too.
Re:I'll wait for Genester (Score:2)
Re:I'll wait for Genester (Score:2)
While I couldn't help but laugh at your post, I also couldn't help but think of the serious truth it may hold. Imagine how the music world got flipped upside down by Napster and its ilk. Now we're seeing those 3D printers get cheaper and more powerful, they can even print electronic circuits now. How long before blueprints are traded over P2P and you simply download them and print out your new iPod?
But this REALLY gets interesting once gene ther
It is NOT a gene sequencer!!! (Score:2, Informative)
Watch out for Fisher Price (Score:2)
The next biotech killer app? (Score:4, Insightful)
No, its the biotech killer app that will start a civil war in 10-15% (average region dependent) of all households on the planet
Over the counter, at your local drugstore, genetic paternity tests.......
Whoever markets the first reliable one will be richer than Bill Gates.
Re:The next biotech killer app? (Score:3, Funny)
Cool... (Score:3, Insightful)
Fix your eyes with friggin' lasers.
Communications the size of a pack of smokes (cell phones)
Bluetooth
The Internet
Video Conferencing (and even Video Telephones)
Terrorists with WMDs
Robot that vaccuums
and now...Toys for Sequencing DNA for Junior. Heinlein et al would be proud
Still waiting for flying (or automatic/autopilot) cars, permanent station on Moon/Mars (I'll accept either), Cancer/Common-cold cure (I'll accept either), humanoid robot for menial tasks around the house, acceptable voice control/communications in conjunction with useful AI computing...etc...
Re:Cool... (Score:2)
When is this supposed to happen. The electrolux vacuum is tempting though.
Re:Cool... (Score:2)
Christ I'm tuning into a luddite, and enjoying it. When do I get chucked off /.?
a bit more advanced version (No DIY though) (Score:2, Informative)
www.iwoot.com
you can get a different but more professional dna in a tin kit
http://www.iwantoneofthose.com/ProductDetails.asp
its not DIY though, its a mail in DNA kit
old news: many DNA science projects (Score:2)
In other news (Score:3, Funny)
reminds me (Score:2)
one could get it on the internet (hoax or truth? no clue)
it was called 'be your own god' and contained all kinds of materials to clone genes for bacterial toxins and stuff. anthrax a go-go
anyways i suspect that, if it ever was available, it won't be now, given the whole 9-11 situation and the anthrax scares and all...
Re: (Score:3, Insightful)
Re:reminds me (Score:2)
i know about Bacillus antracis (though i won't bother to spellcheck the name now
but a kit with the things on plasmid (i presume) is a bit over the top don't you think? it made me wonder then... anyway now, with the sequence probably available at some genomics site (or is that protected too?) it would be a few dyas work to clone and express the (gene encoding the) toxin.
ah well.
blah
and blah
anyway, as i said, no clue whether it was just some urban
Finally an answer.... (Score:4, Funny)
Fisher-Price Cloning Kit? (Score:2)
Some would claim that creating clones with the Fisher-Price Clone Kit is nothing more than "Child's Play," wereas serious people (like William Tenn) would prefer a serious kit.
Remember, kids, only Build-a-Man can build a man!
Re:Wow (Score:4, Informative)
Re:Wow (Score:3, Informative)
You also get to do electrophoresis and take pictures of your product, which is kinda cool. I can just see what's going throuh those kids minds right now....So, how similar are fido and the cat? What if I compare little sister's DNA to mine? Hey, you hold down the dog while I get some blood....oops....
Re:Wow (Score:5, Informative)
Its not quite what it says on the story, its not DNA sequencing its just a DNA seperation kit using the bog standard ethanol prep [exploratorium.edu] which you can do with washing up liquid, salt and a bottle of (80%) Polish vodka. The electrophoresis [nexusresearchgroup.com] step is quite nice using a battery to provide the DC current. However the kit is nothing you could not make yourself (Most of Molecular biology is really quite low tech the main requirement is getting pure reagents to do it with)
Thats not to say its not a cool gift/toy, at the very least the Centrifuge, and Electrophoresis chamber could probably be reused by the budding geekling
here [discovery.com] is the link to the actual product.
Re:A small nit. (Score:2, Informative)
No I'm a molecular biologist I mean 80% by volume (160 proof) anything much less won't precipitate the DNA. I'm in the UK and can buy 80% vodka from my local supermarket. (I plan to buy a bottle and use it when doing demos for the university open day .... granted I'll empty th
Re:Wow (Score:5, Informative)
All it gets you is a pattern of sites that the enzymes cut at, not a sequence. Still, this is how a lot of DNA work (particularly forensics) is done, and it's awesome enough for me to want one (even though I have ready access to the real stuff).
Re:Misleading (Score:2)
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.)
Pro Athlete demographic! (Score:3, Funny)