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Home DNA Sequencing
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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"What's next, the Fisher Price Cloning kit?"
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...
Vincent J. Murphy
Spandex Justice
Why pay when you can do it for free?
Now, your kids can check if you are their real father for themselves.
I think a lot of kids wil be very happy with this information.
--> Insert Funny Sig Here
Unfortunately, this is a bit far from sequencing. All you're doing is taking the raw DNA and making it insoluble in water. So, really, it's a great way to make false snot... which should appeal to the young male sector more anyway. Gross is G00d
I am curious how powerful the centrifuge is in this thing. My mom worked in a med-lab and they had centrifuge repair guys on call in case one started to make funny noises. Unstable high RPM systems of blood and glass can get a little nasty.
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Could any biochemists comment on the likely limitations of this kit? Ok, obviously it's a toy, but what limitations look like they've been placed on this thing? I know we're all making jokes about 'Daddy's not junior's father' but sadly :) I can't see this thing having the resolution to provide that much information.
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?
-- INTX Grouch. http://www.midnightblue.net
This basically extracts DNA and runs whatever natural fragments form across a gel - definitely not sequencing, but certainly cute.
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.
It doesn't work too well, when you light the ring, it doesn't ignite evenly, it just sorta flashes upward from the point where you ignited it, no flaming rings shooting across the room, as cool as that would be.
"Sic Semper Tyrannosaurus Rex."
It would seem that products like this one (or maybe slightly more professional versions) would eventually support distributed human genome sequencing efforts by individuals. More data on the DNA sequences of more people would help scientists, biomed, and pharma types understand the genetic variability of people.
I guess the next frontier is Sequencing@Home with people bragging about how many of their own base pairs or chromosomes they have sequenced.
Two wrongs don't make a right, but three lefts do.
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 which you can do with washing up liquid, salt and a bottle of (80%) Polish vodka. The electrophoresis 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 is the link to the actual product.
It's just gene mapping via electrophoresis, rather than sequencing. The stuff to do it crudely is actually pretty simple and cheap.
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).
Quite simply there is no sequencing ocurring. It's merely separation of DNA molecules. This will just tell you their size. There's not sufficient information in the article or the store blurb for me to figure out if restriction enzymes are being included, which would make things slightly more interesting. In the days before PCR and DNA sequencing was as easy as it is now, genetic tests were done via Restriction Fragment Length Polymorphisms, so your DNA would break up into differently sized bits depending on which sequence was present at a cutting site.
I took a little time to read the description of the kit on Discovery's website. It's much less than the /. post suggested. There's just some chemicals and a toy centrifuge to extract DNA. Actually there are ways to extract DNA with household chemicals, precipitate with isopropanol and spool on a glass or plastic rod.
So far it's only DNA extraction, cool as a science-for-fun thing, but nothing new.
The analysis part (with electrophoresis) seems to be fake (simulated, if you wish). The kit, according to the Discovery website contains
"DNA stain (fabricated to mimic real DNA)".
So, it's just a toy, cool, but nothing that'll allow Junior to test his paternity or do any real DNA analysis. There are educational kits that provide real DNA analysis in a classroom environment (like the Biotechnology Explorer program from BioRad), but they still require teacher's supervision.
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.
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.)
Using HTML in email is like putting sound effects on your phone calls. Just say <strong>no</strong>.
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:
- Microbial and viral sequence data is probably the most immediately useful, because by comparing the sequences of different strains of pathogens (e.g. HIV) we can track the emergence of these strains, figure out when and where they originated, and hopefully control the most virulent strains.
- More excitingly, these little critters tend to have genomes that are really simple; learning, e.g., which genes in a viral genome code for which proteins in its coat allows us to develop new drugs against it. AFAIK, most of the latest generation of AIDS drugs (which don't cure the disease, certainly, but do allow its victims to live much longer and better lives than previously) were developed this way.
- In a similar vein to the first item, it's possible to track the evolutionary development of bigger organisms (e.g., us) by comparing changes in sequences between those organisms and their close relatives (e.g., other primates). This kind of "phylogenetics" has already changed a lot of previous assumptions about various organisms' relationships to each other and their common ancestors; it's not an exaggeration to say it's redrawing our picture of the tree of life. This is, of course, pure science rather than engineering; whether you value knowledge for its own sake is up to you. (And if you're a creationist, then please stop reading; I don't like spending my time explaining things to idiots.;)
- "Bad" gene sequences are the cause of cancer, and of almost every other non-infectious disease we know of. (Sickle-cell, cystic fibrosis, Tay-Sachs, you name it.) Right now, about all we can do is identify individuals who are at higher risk for some form of cancer because of some particular kink in their DNA. That's still important, because it allows those individuals to be more closely tracked and given earlier treatment if and when tumours do appear. However
... - We are at the dawn of the gene therapy era. (Like all ages of exploration, it's risky; so far I think the score is something like two patients cured, twenty killed.) It is entirely reasonable to expect that within a decade or two, we will be able to insert "good" copies of "bad" genes, replacing the genes which cause these diseases. This is the whiz-bang stuff that has everyone so excited.
There's plenty more, but this is the stuff I can come up with off the top of my head and with only half a cup of coffee so far this morning.The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
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.
There is a reason for everything. Sometimes that reason just sucks.
Another poster gave a good explanation of the applications of sequencing. I'll give you a quick explanation of how it is done:
...
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).