3 ms·

so if I'm new to this, how can I use this machine to test out for diseases? That seems like a good first practical use.

deleted 15y ago
[deleted]
rflrob 15y ago
Some diseases will be easier to check for than others. For example, Huntington's Disease [1] is strongly associated with having multiple repeats of a short sequence (CAG) on chromosome 4. You would start by designing PCR primers to the sequence around this repeat, typically aiming for a couple hundred base pairs total. Then, you extract your DNA [2], and PCR out that region. Finally, you run your PCR product on an agar gel, which will separate it by size, with smaller things running faster. If you have a sensitive enough ladder (i.e. a set of DNA pieces with known sizes), you should be able to see measure the size of the product, and from there estimate how many CAG repeats you have. A different project might be to test whether you are infected with, for instance, H1N1/09 influenza (aka swine flu). Using sequences available online, find a segment of DNA that's unique to the strain you think you might have, collect DNA (the mouth swab may even have enough if you're contagious), then PCR out that segment of DNA. It would be nice to have a negative control as well, such that if you get a product, you know it's not just some other segment of DNA that happens to amplify off the same primers. [1] http://en.wikipedia.org/wiki/Huntingtons_disease http://en.wikipedia.org/wiki/Huntingtons_disease [2] Kits available, such as http://www.epibio.com/item.asp?ID=270 http://www.epibio.com/item.asp?ID=270 . Alternately, can do a phenol-chloroform extraction, which would require a centrifuge and access to some nasty chemicals, though might be cheaper per extraction.
deno 15y ago
Comment [dead] for some reason (false positive): http://news.ycombinator.com/item?id=2738007 http://news.ycombinator.com/item?id=2738007
Cixelyn 15y ago
Here's one way of doing it with a PCR machine: 1. First find a risk gene of interest. You can find a gene name via flipping through scientific articles about the disease, and then finding the exact sequence of the gene on NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/inde...). 2. Design primers that amplify around the region of interest. ($15 maybe tops?) 3. Toss everything into a PCR machine and amplify it up. ($3 or so for per-run reagents?) 4. Take your amplified product and send it off for sequencing (another like $10 or so?). When you get the sequence back, compare your sequence to the published sequence and see how it looks! There are a few caveats in primer design, and there are some other ways of detecting disease markers, but this is one easy relatively low-cost approach.

deleted 15y ago

[deleted]

Some diseases will be easier to check for than others. For example, Huntington's Disease [1] is strongly associated with having multiple repeats of a short sequence (CAG) on chromosome 4. You would start by designing PCR primers to the sequence around this repeat, typically aiming for a couple hundred base pairs total. Then, you extract your DNA [2], and PCR out that region. Finally, you run your PCR product on an agar gel, which will separate it by size, with smaller things running faster. If you have a sensitive enough ladder (i.e. a set of DNA pieces with known sizes), you should be able to see measure the size of the product, and from there estimate how many CAG repeats you have. A different project might be to test whether you are infected with, for instance, H1N1/09 influenza (aka swine flu). Using sequences available online, find a segment of DNA that's unique to the strain you think you might have, collect DNA (the mouth swab may even have enough if you're contagious), then PCR out that segment of DNA. It would be nice to have a negative control as well, such that if you get a product, you know it's not just some other segment of DNA that happens to amplify off the same primers. [1] http://en.wikipedia.org/wiki/Huntingtons_disease http://en.wikipedia.org/wiki/Huntingtons_disease [2] Kits available, such as http://www.epibio.com/item.asp?ID=270 http://www.epibio.com/item.asp?ID=270 . Alternately, can do a phenol-chloroform extraction, which would require a centrifuge and access to some nasty chemicals, though might be cheaper per extraction.

deno 15y ago

Comment [dead] for some reason (false positive): http://news.ycombinator.com/item?id=2738007 http://news.ycombinator.com/item?id=2738007

Cixelyn 15y ago

Here's one way of doing it with a PCR machine: 1. First find a risk gene of interest. You can find a gene name via flipping through scientific articles about the disease, and then finding the exact sequence of the gene on NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/inde...). 2. Design primers that amplify around the region of interest. ($15 maybe tops?) 3. Toss everything into a PCR machine and amplify it up. ($3 or so for per-run reagents?) 4. Take your amplified product and send it off for sequencing (another like $10 or so?). When you get the sequence back, compare your sequence to the published sequence and see how it looks! There are a few caveats in primer design, and there are some other ways of detecting disease markers, but this is one easy relatively low-cost approach.