Polonator Frequently Asked Questions
Is the Polonator for sale?
Yes, we are now accepting orders.
What took so long?
We determined last year that an upgrade of our fluidic system was in order. In parallel with that, the flow cell was redesigned to better align it with our forward roadmap, and the decision was made to provide a pair of easy to use GUIs to simplify the user experience. There was a lot of design and coding effort required to implement these changes. Last year, we began shipping Polonators to early adopters outside of the Church Lab, and between then and now we have been using the feedback from our users to address any and all issues that they reported. We insisted that the platform be robust before we moved to general release. We and our early adopters are very pleased with the progress, and can now offer a robust, high performance instrument to the research community.
How much does it cost?
As a result of system improvements, the current sell price is 170,000 USD.
What is the delivery time?
We can supply the Polonator in six weeks after receipt of order.
What is the read length?
The current read length is 26 bases, in a 13 + 13 base paired end read. There is a 3-4 base gap in each read; the Polonator reads seven bases on the minus side and six bases on the plus side of each tag. One of our early adopters (Jeremy Edwards of the University of New Mexico) has extended the minus side to eight bases, expanding the read length to 28 bases. Extensive work has been done on more significant expansions of read length (see below).
What is the output per run?
A run currently generates 8 – 10 million mappable reads per lane (unenriched), with eight lanes per flow cell, and either one or two flow cells per run. For a dual flow cell run, that results in about 150 million mappable reads per run. Expressed in bases, that is about 4 -5 BGp. Enrichment will about double the output to 8 – 10 Gbp, but does not improve the cost per base.
How long does a run take?
The duration of a run is currently about four days. We expect that to shrink to about two days when our imaging upgrade (see below) is released, but to return to about its present duration when our 48 bp longer reads are introduced.
What is the accuracy?
The accuracy of mappable reads is a function of specific algorithms within the aligner, as well as the performance of the sequencing instrument. We have recently uploaded quality data to this website; click on the DATA tab to review this data. In general, the best 92% of the mappable reads have a mean accuracy of above 98%. Evaluating accuracy claims from different systems requires careful comparison of their respective methodologies, but the information provided on the DATA tab of this site should provide sufficient detail to properly assess the accuracy of Polonator data.
Are you offering reagent kits?
We had been planning on offering reagent kits for the current 26 bp (13 + 13) paired end sequencing chemistry. Given the likely introduction of more attractive longer reads (see below), we chose not to do a quantity buy on the 26 bp kit components. In the interim, we provide explicit information on kit components (base sequence, concentration buffer, enzymes, suppliers, etc) to allow users to cost effectively source reagents themselves.
Where can I find detailed protocols for your current sequencing chemistry?
PDFs of each of the Polonator protocols are available on the Protocols Tab of this web site.
Where are you with respect to longer reads?
Recent testing of some longer read approaches has been promising, and we now anticipate the release of a 48 base paired-end read (24 + 24), as well as a 24 bp fragment (single-end) read during 2009, hopefully by Q3. We will be providing reagent kits for this chemistry when it is released. Work continues, both within the Church Lab and among our early adopters, on a variety of cyclic ligation based long read chemistries, as well as polymerase based approaches, with the goal of further extending read length.
What does the Polonator forward roadmap look like?
As mentioned above, work on longer reads is ongoing, with an extended read chemistry release expected this year. A straightforward upgrade to our imaging system in Q3 will increase the imaging speed from 10 to 30 frames per second, while continuing to fully process all images in real-time. A major system enhancement relates to removing the inefficiencies and cost of emulsion PCR. We have licensed IP from the Church Lab on rolonies (rolling circle colonies), and will be replacing the current randomly arrayed, bead-based, emulsion PCR with rolonies on ordered arrays. This should provide a substantial efficiency gain, since currently only one in six beads provide a clonal signal. An upgrade to higher numerical aperture optics may also be phased in at this time. As we adopt longer read chemistries and tighten the pitch on the ordered arrays, we expect that the output per run will climb to over 100 Gbp in 2010.
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