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Well, Helicos is certainly not the only game in town in the current crop of new sequencing tech. Each of the new technologies has its strengths and weaknesses.
by JunkDNA 17y ago
Well, Helicos is certainly not the only game in town in the current crop of new sequencing tech. Each of the new technologies has its strengths and weaknesses. This is clearly a bit of PR on their part. I believe their technology is more expensive than their competitors, and until a week or so ago, I think they had yet to get anyone to buy one of their sequencers.
The main problem with DNA sequencing is that nobody has really commercialized a way to "passively" read the sequence. All of the currently marketed technologies involve some kind of chemical fluorescence process where little bits of DNA are used as templates. The templates are extended base by base with fluorescent-labeled bases. Between the chemical reaction, and the need to accurately measure the fluorescence, you can really only go so fast and maintain accuracy.
Once you do the chemistry and have the raw data, you've really just got TONS of tiny sequences (known as "short reads"). These reads are anywhere from 20 - 30 bases or so, depending on the technology. They need to be assembled into a complete genome by figuring out where they overlap with each other. This is a computationally expensive problem, but it's reasonably doable with a small Linux cluster.
This is a huge improvement in sequencing (most notably, it removes a lot of human intervention). That said, large-scale sequencing is still in its infancy. In my opinion, all of this is a stopgap until someone is able to engineer a process that gives really long reads. There are numerous problems with assembling short bits of sequence. Most notably, there are lots of areas in the genome which have a huge amount of repeated DNA sequence. Since reads from neighboring parts of the repeated sequence can be identical, there's often no way to know how many are duplicated. Pacific Biosciences claims they can sequence 2.5 kilobases of a single molecule with their technology (not yet on the market). Something along those lines could really change the equation.