The Church Lab and Dover Systems have collaboratively designed the G.007
instrument to optimally implement polony sequencing
protocols, and will be employing it in the Lab’s upcoming
Genome Project. The “Polonator” seamlessly
integrates the following subsystems into a compact,
desktop instrument: motion, laser autofocus, optics,
illumination, flow cell mounting, fluorescence, digital
imaging, fluidics, temperature control, electronic
control, data processing, user interface, and the
structure/skins. Despite a high degree of integration,
all subsystems are completely modular, and can be
easily upgraded as the instrument evolves.
The G.007 protocols have
been developed by the Church Laboratory,
which pioneered the polymerase colony
(polony) sequence by ligation method. These
tested, revision controlled protocols are
freely available for download, and include
paired-end-tag (PET) genomic shotgun library
construction, emulsion PCR, emulsion breaking,
bead enrichment, bead capping, coverslip
aminosilanation and arraying, and polony
sequencing protocols. The latter is designed
for general-purpose genomic sequencing, and
generates a read length of 26 bases.
Dover Systems will be supplying complete reagent kits
to implement the G.007 polony sequencing
protocol, as well as the upstream paired-end-tag
library construction, emulsion PCR/bead capping,
and bead enrichment protocols.
Innovations include a very low cost PCR
polymerase, as well as oligos with license free
“Freedom Fluors”. We have gone to
lengths to assure the lowest possible reagent
costs for the initial kits, with significant further
reductions expected as scale is achieved.
The Polonator software has
been developed by the Church Laboratory, and is
the result of multiple programmer-years of focused
effort. The source code is freely available for
download, and is fully commented and open-source.
Users may either use it without modification, or
improve and extend it as they see fit. The software
is composed of two separate programs, which
work in synchrony, each with its own dedicated 1U
computer. One program handles image acquisition
and instrument control, while the other process
images and generates base calls.
The Polonator flow cells are
the result of extended development at the Church
Lab, using both physical trials and advanced CFD
(Computational Fluid Dynamics). Two flow cells
are mounted within the instrument; for maximal
throughput, one undergoes biochemistry while the
other is imaged. Each flow cell has 18 individual
wells, with a total of over 1 billion streptavidin
coated polystyrene beads. Both flow cells slide
easily into place and dock automatically, with no
need to attach tubes or fittings.
Support & Community...
Dover Systems offers multiple response levels of
direct user support, including instrument hardware,
protocol implementation, and software. In contrast
to current “black box” offerings, with proprietary
protocols and reagents, all aspects of the Polonator
system are open and fully accessible. We encourage
and actively support the growth of a flourishing
user community that freely shares its feedback
and improvements, advancing and extending the
Polonator system and its capabilities.