Reduction in cost of DNA analysis

Discussion in 'Biology & Genetics' started by Billy T, Jun 9, 2007.

  1. ElectricFetus Sanity going, going, gone Valued Senior Member

    Messages:
    18,178
    I did not say it was used for that. He wanted to know where RNA "came from" I explained were I comes from a Biological and biotechnological stand points. Personally I don't think I've heard of many uses for synthetic large RNA oglionucleotides
     
  2. Google AdSense Guest Advertisement



    to hide all adverts.
  3. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    In OP I stated:
    The shares have again doubled in less than a year. Graph of share price is essentially an uninterupted upward slope that double the value in about 11 months. If this keeps up, it is hard to see how the cost of DNA analysis can also be dropping even faster. Ain't technoloy great!

    Please Register or Log in to view the hidden image!

     
  4. Google AdSense Guest Advertisement



    to hide all adverts.
  5. CharonZ Registered Senior Member

    Messages:
    786
    Just wondering, have you checked the share price of Roche? Their sequencer (the 454) has actually been used to sequence a number of whole genomes now (for which scaffolds already exist). Unfortunately I am not that familiar with publications based on the ILMN systems, as genotyping (as opposed to sequencing) is not really my field.
     
  6. Google AdSense Guest Advertisement



    to hide all adverts.
  7. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    Not often. Roche is diversified "big Pharma" and that does not interest me either financially (in part because lots of big pharma's drugs are going off patent)* nor as motivation to learn more about the "magic bullets" that are being developed. I have financial interest generics Teva, Barr and Novaris, whch is also sort of "big pharma." I keep looking at Dr. Ready and Mylan, but do not own either, yet. (Have missed buying Dr. Ready a few times, by "bottom fishing" too far below market.)

    I know GE makes a machine also; Think it is cheaper, but not as good as Illumina's. - GE is about as diversified as it gets, so sales of that machine do not budge the stock.
    ----------
    *Also, as I fear dollar collapse, I like high risk early developers as their high risk is already priced in and so large that the dollar dropping risk is relatively less important.
     
  8. CharonZ Registered Senior Member

    Messages:
    786
    I actually do not know if GE is currently developing a new sequencer. The sequencers that they currently sell use the old Sanger technique though, which is actually usable for whole-genome sequencing. I have heard that one company (forgot which) is currently developing a system based on Sanger but is highly parallelized. In theory it should have all the advantages of the Sanger system as well as having the output of the newer systems (like 454 or Solexa).
    If it gets out it will again be big news for scientists at least. Depends a bit on the price, too, though.
     
  9. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    If you remember which (best not to try - it will come to you) please send me a PM. I will look into it and perhaps sell some ILMN and buy it with the funds to diversify. - Never can tell what you guys will like and have funds to buy.

    Please Register or Log in to view the hidden image!



    Thanks for the information.
     
  10. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    I own shares in StarPharma. I do not know if important, or of interest as will facilitate research but they recently announced text I compressed below. Any comments as to the significance, if any?

    "... a research reagent kit called NanoJuiceTM Transfection Kit for transporting DNA into cells, was developed under a license between Starpharma’s subsidiary Dendritic Nanotechnologies and EMD Chemicals Inc., an affiliate of Merck KGaA, Darmstadt, Germany.
    Under the commercial agreement, Starpharma retains full rights to all in vivo aspects of transfecting DNA and other nucleic acids such as siRNA with products based on Priostar® technology Starpharma supplies.
    The NanoJuiceTM Transfection Kit will improved transfection efficiencies with low toxicity to cells and flexibility in the conditions of transfection.
    It is suitable for all types of cell growth media and does not require that the medium be changed after addition, thereby affording researchers substantial savings in time and money.
    Starpharma’s Priostar® dendrimers are highly branched spherical molecules with a high concentration of active groups on the surface that bind to DNA. It is the only reagent available that has been optimized for different cell lines through the use of different sizes of dendrimer.
    The kit was designed to achieve efficient transfection of mammalian cells, especially those derived directly from tissues (so-called ‘primary’ cells), as well as the cell lines that are traditionally difficult to transfect.

    EMD to launch a related siRNA transfection reagent kit later in 2008. ...
     
  11. CharonZ Registered Senior Member

    Messages:
    786
    Now regarding whole genome sequencing:

    I have mentioned earlier DNA sequencing with immobilized polymerases? According to the developer they aim to make it possible to sequence the human genome with a material cost of only 1000$ (sequencer not included, of course).

    Another direction is the use of nanopores to enable sequencing in zeptolitre volumes. This allows an unprecedenced possibility to parallelize the sequencing reaction. In theory (I do not now the most recent benchmarks) one could sequence a whole human genome within a day or two. Unfortunately the technique are progressing faster than the ability to actually deal with the data. Ah well...
     
  12. ElectricFetus Sanity going, going, gone Valued Senior Member

    Messages:
    18,178
    The holy grail will be a on-chip DNA sequencer that runs single stranded DNA through a nanometer channel under atomic force probes, or related device that can read a single DNA molecule, the read speed could be hundreds of thousands to millions of base pairs per second. The time and price to read a human genome would be in hours and a few dozen dollars.
     
  13. Hercules Rockefeller Beatings will continue until morale improves. Moderator

    Messages:
    2,720
    Man, I’m so far behind in this area. I have little idea what you’re talking about. I remember back when I was a student having to do manual DNA sequencing.

    ie. performing 4 separate reactions for each of the different [sup]35[/sup]S labelled ddNTPs, casting a big polyacrylamide gel, running the reactions side-by-side for several hours, drying the gel, exposing a x-ray film sheet, developing the film……

    …then manually reading down the DNA ladder of the film and recording the sequence by hand!

    Please Register or Log in to view the hidden image!



    Please Register or Log in to view the hidden image!



    The technique has come a long way since then (thank god!).
     
  14. ElectricFetus Sanity going, going, gone Valued Senior Member

    Messages:
    18,178
    And believe it or not their still further to go!
     
  15. CharonZ Registered Senior Member

    Messages:
    786
    Well, I also remember sequence manually, however I already had fluorescent dyes instead of isotopes.
    This strikes me a bit of odd:

    Where did you find the value of millions bases per second?
    By chance I talked to some guys actually trying to realize sequencing via pulling DNA through nano pores and measuring forces with an AFM and I have an AFM, too. From what I know about AFMs and what I heard from the others is that the main advantage would be low cost and long read length once realized, however I find it hard to believe that a speed of million bases a second could be realized, given the slow measurement speed of an AFM.
    However, another promising approach which might be faster is based on measuring the distribution of traverse electrical currents as the DNA passes through a pore. The reading speed would be much higher, but would have to be repeated to reduce errors.

    In any case, afaik these techniques have not been applied to real genome sequencing yet. Much of the published work have been conceptual or proof of principle at best.
     
  16. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    What is the typical distantance along the DNA from one base pair to the next? How does that compare to wave length of blue light? Is there reason to think that the pairs would have different optical properties? {transimison, reflecdtion of optical activity (rotation of polarization plane)}

    Perhaps even some Ultra Ultra high frequency sound scattering by the base pairs could be a probe? One has the advantage one is only trying to determine which of only two (I think) possible links is present at each station along the DNA chain.
     
  17. ElectricFetus Sanity going, going, gone Valued Senior Member

    Messages:
    18,178
    Wave length of blue light: 400nm
    Distance between basepairs: .34nm
    Sorry but at those sizes you would need an atomic force microscope, Electrons or high energy x-rays would complete obliterate the DNA to see base pairs on a single strand. There are several alternatives though like using a transmembrane protein and measuring the voltage across the protein as the DNA runs through it, or labeling each and every base pair with a fluorescent tag and using some advance optics to read each base pair.
     
  18. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    Thanks. Obviously an optical approach will not work (and shorter wavelenghts will destory instead of observe)

    I do not know much about it but the AFM seems to have great problems too. The effect is very strongly dependent upon the distance from the tip to the atoms being observed. (In practice, I think, they keep the separation essentially constant and measure the tip movement required for this.) Would not the twist of the DNA make this impossilble? I have only, some years ago admittedly, seen AFM applied to rare irregularities on cleaved crystal surfaces - as perfect planes as can physically exist.
     
  19. ElectricFetus Sanity going, going, gone Valued Senior Member

    Messages:
    18,178
    the idea is to have a micro chip with nanometer channels that force DNA to run through the channel were something like AFM probes are placed along the sides. The ideas is limited by chip manufacturing technologies which would require making chips with single nanometer tolerances, in short it still a few years away.
     
  20. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    Would the section of thechannel where AFM tips are be deeper than it is wide? (so the DNA twists to keep the (sugar?) backbones at the top and bottom of the channel and let the tip(s) "feel" the cross links?
    What "aspect ratio is typical of DNA cross section? If the one of the two possible (normal) cross link pairs is significantly longer than the other, perhaps the force required to pull the chain thru a hole slightly greater than the average (in cross section, not along the length) radius of the DNA can tell what the cross link is at that station? I suspect it is much easier to make a precise hole than a precise channel but while my eyes are are still very good (especially for fine work as I am near sighted) I will let you "thread that needle"

    Please Register or Log in to view the hidden image!

     
  21. ElectricFetus Sanity going, going, gone Valued Senior Member

    Messages:
    18,178
    Well to be honest it would only be AFM like the probes would have to work by a very different mode of operations because the DNA would be in some kind of organic solvent which would "blind" a normal AFM. A channel is needed because many probes are needed in series to re-read and correct out the noise. As for the hole idea that being work on by another group that is trying to use a transmembrane protein as the "hole" and measure voltage changes as different base pairs run through it, again its problem is lack of noise cancellation through re-reading.
     
  22. Billy T Use Sugar Cane Alcohol car Fuel Valued Senior Member

    Messages:
    23,198
    Oh. In a liquid? That is a bitch. Let's work in vacuum to avoid discrimination between effects of liquid and cross linking molecules:

    How about holding it, at the ends, in "micro tweezers" (glue dots?) and moving it behind very tiny hole in metal foil while shooting electrons thru the hole with precisely controlled energy and measuring their energy loss as different pairs in the DNA chain are transversed by the electrons etc.
     
  23. ElectricFetus Sanity going, going, gone Valued Senior Member

    Messages:
    18,178
    Trying th pull DNA across anything in a vacum would be like trying to pull tap along a surface, the DNA would stick to just about any surface. let alone if you can keep it straight the DNA would break, the fluid allows you to pump via ionic pull many short stains (short as in maybe 100,000 bp) of dna one at a time through your detector, thus breaking is not a issue, you just connect the separate pieces together on a computer.
     

Share This Page