To Rocketman, Boyce Burge, V1, or anyone else who wants to participate:
First of all, thank you for the high quality, informative, and useful information that you three have contributed on AFFX and INCY on this thread, the AFFX thread, and the INCY thread. You are gentlemen and scholars. This is SI at its best.
As someone who is not even remotely involved with this technology, I have a couple of theoretical questions. (I own stock in AFFX and INCY, like both companies, and feel there could be room and roles for each.)
Rocketman, in his reporting of INCY's annual meeting, wrote: "AFFX uses ~20 bp probes on the chips built up with photolithography/masking technology. Synteni uses 1000 bp probes which are spotted down on the GEM chips. While both companies can put 10,000 probes on a chip, they estimate AFFX can only cover ~1500 genes on a chip because they need more probes for each gene because redundancy of ESTs from the same gene needed due to the non-specificity of the short probe length."
My questions:
1)Where is Synteni obtaining these longer bp probes?
Does this mean that the cost of producing the chips will be higher for Synteni compared to the automated process of AFFX?
2)I would think that there is a trade off in having a longer bp probe. While you could fit more genes onto a single chip, I would think that there wouldn't be much difference in the annealing of a 1000 bp probe with its intended dna fragment versus a dna fragment that differs by only one or two bps. i.e. this longer probe may be less sensitive to SNP's than the shorter probes of AFFX. A mismatch of one in a thousand bp's might not be as noticeable as a mismatch of one in twenty. It isn't a criticism of either chip. Depending on the genetic question you want to answer, you may want a chip set that can look at an entire genome at lower resolution (?Synteni) or a chip set that looks at a more limited segment of the genome at single bp resolution (?Affx).
I would appreciate any thoughts or comments.
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