[Automated-sequencing] Sanger sequencing obsolete?

Phillip SanMiguel pmiguel at purdue.edu
Tue Jun 21 20:06:26 EST 2005


Not for a while anyway. But I'm getting the impression that some of the 
$100,000 and $1000 human genome sequence methodologies are beginning to 
pay off.

Anyone plunked down half a million dollars for a 454 Life Sciences 
sequencer? See:

http://454.com

Well, that web page only really works with Internet Explorer. But the 
take home is that it is a sequencer that does about 200,000 reads per 
run. But median read length is 100 bases. Library construction needs to 
be on beads that are centrifuged into individual wells of a 1.6-million 
well "pico titer plate". The actually sequencing is done via 
synthesis/pyrosequencing/luciferase reactions. As each base is added (if 
one is added) light is emitted and the machine somehow detects the light 
and the pico titer plate position of where the light is emitted.

When I heard about this technology, I searched the web and found the 
following synopsis:

http://www.up.ac.za/organizations/societies/psana/DNA_Sequencing_Industry.pdf

But it might be a little out of date. Basically the take-home from that 
pdf is:

        Solexa
        Location: Essex, UK.
        Founded: Spun out of the University of Cambridge
        in 1998.
        Technology: Single-molecule sequencing utilizing
        DNA cluster technology. Arrays will be
        capable of sequencing 100 million sample
        DNA templates per cm2 of chip.
        Solexa's Technology 
http://www.up.ac.za/organizations/societies/psana/Solexa's_Technology.pdf
        Read Length: 25-30 bases.
        Expected Launch: Expects to be sequencing
        genomes next year.

        Helicos BioSciences
        Location: Cambridge, Mass.
        Founded: May 2003.
        Technology: Single-molecule sequencing in
        which up to 300 million fragments can be
        attached to a single slide, enabling 10x
        coverage of the human genome in a single
        experiment.
        Read Length: 5-10 bases now, but working
        on increasing that to 25 bases.
        Expected Launch: Undisclosed.

        GenoVoxx
        Location: Lübeck, Germany.
        Founded: Spun out of the University of Lübeck
        in May 2002.
        Technology: AnyGene technology utilizing
        the sequencing-by- synthesis method.
        Read Length: 45 nucleotides, but with a 30%
        error rate.
        Expected Launch: Aiming for 2006.

        454 Life Sciences
        Location: Branford, Conn.
        Founded: Spun out of Curagen in 2000.
        Technology: Sequencing-by- synthesis method
        whereby beads are attached to individual
        strands of DNA and placed in individual wells
        of its PicoTiterPlate.
        Read Length: Short readlengths. Company researchers
        have achieved production
        readlengths of 100 bases.
        Expected Launch: Q1 2005.



-- 
Phillip





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