Comment Re:processing time claim is very optimistic. (Score 3, Informative) 95
I imagine they can do it in the time they say. I also imagine the results are very simple, like looking at one STR sequence and counting how many lengths of it are in the person's genome in a process similar to qPCR, less RFLP/southern, as parent seems to think. Despite what TFA might imply, I don't think there's endonuclease digestion involved. I may be wrong, and they could have a really, really fast breifcase thermocycler making this work. Maybe, doubt it.
I'm not any kind of STR expert, but from cribbing Wikipedia http://en.wikipedia.org/wiki/Short_tandem_repeat, here's my impression of what's going on with this kit:
1. get cells = blood and semen. yum. In fact, I'd infer this kit is probably a "semen-only" deal in practice, which makes isolating the DNA that much easier, since semen is largely DNA.
2. isolate DNA. Do it yourself, kids! (http://learn.genetics.utah.edu/units/activities/extraction/) 2-5 minutes with a kit.
3. PCR. Here's where things get interesting. What are their primers? I think they're using 5-10 nucleotide STR sequences that are already conjugated to a fluorescent dye. Since STRs for human identification use are just, according to wikipedia, 4-5 STRs (10-50 nucleotides) long, each cycle can probably be as short as 30 seconds. With ramping the temperatures we can call that 1 minute per cycle. How many cycles do we need? 10 cycles gives us 2^10 copies of the original STR, that's (biologist math)1000 copies(/biologist math). Add 2 minutes for our hot-start polymerase, and that's 12 minutes for PCR. Whoo! It well may be less, i.e. shorter elongation, fewer cycles. This is where they're claiming to save time, so who knows.
4. electrophoresis. Undoubtedly capillary, you can see it in the photo (at least I can), and since we're looking at stuff that's only 75 nucleotides max, can be done very quickly. I don't really know capillary gel electrophoresis, but it apparently kicks the shit out of slab gel electrophoresis: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=330505. We'll call that 10 minutes, lol. Could be a bit more? Balances with the PCR.
5. Of course, we added a 10-100 nucleotide standard conjugated to a different fluorescent species from the primers (i.e. the primers glow green and the standard glows red), so we can use our shitty little built-in 2-wavelength spectrophotometer to see where our unknown sample's bands are.
And now we have our data! And that only took... 25 minutes! Of course, this isn't a full-blown RFLP, like parent seems to assume. But just for doing a quick-and-dirty count of STRs, this could work. That's how I'd do it. Maybe I just invented a competing type of kit, lol. In any event, looking at the picture, I get the feeling their pipettes are crap.
Note this doesn't show how many repeats of a given legth the accused has, so the asshole could have 3 5-repeat ones and 2 4-repeat, and the machine would show that as being the same as a person with 1 of each. Also, they may use more fluorescent dyes to look at more STR sequences without too much difficulty. But in general, the samples will be unclean at best, total crap more often than they'll like to admit, and, in the end, only good as a blood-type-and-then-some test. How juries will react to this, I don't know.
To get even farther from parent, the real threat to your privacy is coming from gene chips, the next generation of sequencing technology. This kit is comparatively rudamentary, and obviously expensive. Yet more overhyped crap, whee!
I'm not any kind of STR expert, but from cribbing Wikipedia http://en.wikipedia.org/wiki/Short_tandem_repeat, here's my impression of what's going on with this kit:
1. get cells = blood and semen. yum. In fact, I'd infer this kit is probably a "semen-only" deal in practice, which makes isolating the DNA that much easier, since semen is largely DNA.
2. isolate DNA. Do it yourself, kids! (http://learn.genetics.utah.edu/units/activities/extraction/) 2-5 minutes with a kit.
3. PCR. Here's where things get interesting. What are their primers? I think they're using 5-10 nucleotide STR sequences that are already conjugated to a fluorescent dye. Since STRs for human identification use are just, according to wikipedia, 4-5 STRs (10-50 nucleotides) long, each cycle can probably be as short as 30 seconds. With ramping the temperatures we can call that 1 minute per cycle. How many cycles do we need? 10 cycles gives us 2^10 copies of the original STR, that's (biologist math)1000 copies(/biologist math). Add 2 minutes for our hot-start polymerase, and that's 12 minutes for PCR. Whoo! It well may be less, i.e. shorter elongation, fewer cycles. This is where they're claiming to save time, so who knows.
4. electrophoresis. Undoubtedly capillary, you can see it in the photo (at least I can), and since we're looking at stuff that's only 75 nucleotides max, can be done very quickly. I don't really know capillary gel electrophoresis, but it apparently kicks the shit out of slab gel electrophoresis: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=330505. We'll call that 10 minutes, lol. Could be a bit more? Balances with the PCR.
5. Of course, we added a 10-100 nucleotide standard conjugated to a different fluorescent species from the primers (i.e. the primers glow green and the standard glows red), so we can use our shitty little built-in 2-wavelength spectrophotometer to see where our unknown sample's bands are.
And now we have our data! And that only took... 25 minutes! Of course, this isn't a full-blown RFLP, like parent seems to assume. But just for doing a quick-and-dirty count of STRs, this could work. That's how I'd do it. Maybe I just invented a competing type of kit, lol. In any event, looking at the picture, I get the feeling their pipettes are crap.
Note this doesn't show how many repeats of a given legth the accused has, so the asshole could have 3 5-repeat ones and 2 4-repeat, and the machine would show that as being the same as a person with 1 of each. Also, they may use more fluorescent dyes to look at more STR sequences without too much difficulty. But in general, the samples will be unclean at best, total crap more often than they'll like to admit, and, in the end, only good as a blood-type-and-then-some test. How juries will react to this, I don't know.
To get even farther from parent, the real threat to your privacy is coming from gene chips, the next generation of sequencing technology. This kit is comparatively rudamentary, and obviously expensive. Yet more overhyped crap, whee!
