[ECO]

ECO: Yes, the initial chemistry is 13 bp x 2. At a more granular level, we read 7 + 6 bases from each of two tags; the reads are not contiguous, since 4-5 bases of the 17 - 18 bp tags remain unread. I have written and been sitting on a character-based (PDF) run through the biochemistry; I've been meaning to post it to the Polonator.org site, and will do so shortly, but would post it here for the first time if I knew how. Do you support attachments? I don't see the icon to do this.

Kevin

Not sure why you can't post attachments, unless it's too big, or you're not going to "Post Reply" (the small "quick reply" box at the end of the thread does not support attachments).

I have the PDF limit at 2MB now...let me know if that's not big enough. If you want to make it a new thread that will probably be best and easiest for people to find.

[Kevin McCarthy]

ECO: Ahh, I just saw that I am not yet cleared to post attachments. Resolve this, and I will post the base by base protocols PDF forthwith.

I also forgot to respond to your question regarding bead count. The flow cells were recently redesigned to better match the biochemistry time to the imaging time, among other things. The previous design had 18 circular wells of 15 mm diameter, fed in parallel from a fluidic perspective. The new flow cells have eight linear lanes (also fed in parallel) of 224 mm^2 imaging area each, with the ability (as had the previous 18 well design) to load independent libraries in each lane. We are still optimizing bead loading, but a fair starting estimate would be 7 to 10 e8 beads per flow cell (a run can consist of either one or two flow cells, but the run time is independent of the flow cell number).

Kevin

[Kevin McCarthy]

ECO: Yes, the initial chemistry is 13 bp x 2. At a more granular level, we read 7 + 6 bases from each of two tags; the reads are not contiguous, since 4-5 bases of the 17 - 18 bp tags remain unread. I have written and been sitting on a character-based (PDF) run through the biochemistry; I've been meaning to post it to the Polonator.org site, and will do so shortly, but would post it here for the first time if I knew how. Do you support attachments? I don't see the icon to do this.

Kevin

[ECO]

Kevin, glad to hear it's beginning to come out strong!

The launch chemistry is still 13bp x2, correct? Any comments on how many beads you're looking at per flow cell?

[Kevin McCarthy]

Samuel: Thank you for your interest in the Polonator. We have been busy over the last few months implementing some changes to the fluidics sub-system, the flow cells, and the software. It's been a bit intense, but I'm thrilled to report that the Polonator design is now frozen, and appears from everything we can see to be delivering on its promise. The Church Lab has been extremely rigorous in their testing of the Polonator, and commented recently that "We don't have to fiddle or tweak anything... We just hook them up, load flow cells, and run... they're perfect". Given the very high standards of the Lab, that's music to our ears.

Now that they have fully functioning Polonators, the Lab has begun to qualify the starting (26 bp paired end tag) biochemistry on the instruments. They are currently optimizing both the run biochemistry (which takes place within the instrument), as well as the upstream protocols. They are not yet ready to provide performance data, but we expect that this will be available in the near future. We plan an aggressive road map to drive performance upwards over time, but also recognize the need to put a stake in the ground soon with an initial set of performance data. This will be posted on the Polonator.org web site as soon as it is available.

We are shipping several more Polonators to our early adopters over the next couple of weeks, but we expect a bit of a pause before we enter wide release. The Church Lab is in one sense too competent; they and we agree that we need at least two of our independent early adopters to both confirm that the instrument and biochemistry are easy to use and reliable, and that they can readily replicate the Church Lab performance data, before we can begin to accept orders from the broader community. We have both inventory on hand and work in process to support initial demand, and are deploying the Danaher Business System's cellular manufacturing precepts to flexibly ramp capacity as required. Our lead time target is four weeks, but the backlog of potential users might skew this.

Stay tuned!

Kevin

[Samuel Kim]

Any updates

Hi, Kevin

Any updates on the performance of Polonator?

We are interested in evaluating one. What will be the lead time?

Regards,

Samuel.

[Kevin McCarthy]

I replied earlier, but for some reason it didn't seem to post. Tweaking of the system has taken longer than we expected, although the quality of feedback from the team at the Church Lab has been fantastic. We have redesigned the fluidics sub-system in response to that feedback, and the new design is much more symmetric and significantly reduces software complexity. There have also been changes related to the flow cell design and a restriction enzyme. We've also had reagent process licenses to secure, which proceeds slowly. My latest estimate would be that performance data would be available around the beginning of August.

[ECO]

Any Polonator updates?

[Chipper]

Ok, I am certainly not in the position to order any instrument at this time, but who knows, maybe for the I.008 or J.008... Perhaps it would be wise to offer a G.007x with $100K or so of reagents, the cost of the instrument is actually so low that it does not qualify for some "expensive equipment" grants...

[Kevin McCarthy]

Horigen: No, the elusive $1000 genome won't be delivered by a G.007. Perhaps the I.008 or J.008; but that would be entirely speculative at this point. We do have a road map for backwards retrofittable enhancements to the G's that would preserve the value of your investment as the platform drives throughput ever higher.

Ola: Reagent costs will drop as kit demand builds; quantitative details aren't yet available. At the low price point we have achieved for the instrument ($150K), we cannot support "try out" service. You will either need to take a leap of faith and buy one, or wait until enough third parties have published or otherwise endorsed the platform to feel justified in making a commitment.

Kevin

[Chipper]

Thanks for the update. It is not like the other sytems didn't have initial problems I guess... I am just curious, what sort of scale are you talking about in order to get the costs down? And let us know if you are going to offer some kind of "try-out" service...

[horigen]

Ola: Things always go a little slower than one would wish... The initial G.007 Polonator delivered to the Church Lab in February underwent some serious tire-kicking. The Lab has very high standards. While most of the system was awesome, they found a few details that did need to be addressed. We beavered away on those, and delivered a fully updated G last Friday. At the same time, the Church Lab needed to complete their software, reflecting some of the improvements. They have now done so, and are just now beginning sequencing runs. These will yield data shortly, although this will be first pass, and won't be optimized for the platform for several weeks. We have also been making progress on licensing issues, although a firm out-of-the-gate reagent kit cost is now looking like the beginning of next month. There is also a real trade-off here between scale and cost. Costs will go down substantially once we begin to acheive scale, but we can't do this from day one. Bear with us; it will be worth it!

Regards,

Kevin

Means it's very possible for G.007 Polonator to get a $1000 genome?

[Kevin McCarthy]

Ola: Things always go a little slower than one would wish... The initial G.007 Polonator delivered to the Church Lab in February underwent some serious tire-kicking. The Lab has very high standards. While most of the system was awesome, they found a few details that did need to be addressed. We beavered away on those, and delivered a fully updated G last Friday. At the same time, the Church Lab needed to complete their software, reflecting some of the improvements. They have now done so, and are just now beginning sequencing runs. These will yield data shortly, although this will be first pass, and won't be optimized for the platform for several weeks. We have also been making progress on licensing issues, although a firm out-of-the-gate reagent kit cost is now looking like the beginning of next month. There is also a real trade-off here between scale and cost. Costs will go down substantially once we begin to acheive scale, but we can't do this from day one. Bear with us; it will be worth it!

Regards,

Kevin

[Chipper]

Any news from the performance testing?...

[Kevin McCarthy]

Ola: We have approximate costs determined for the reagent kits, but we can't finalize these until our volumes are nailed down, and some licensing discussions are completed. The G version is undergoing performance testing now, which will allow us to pin down the reagent volumes. I would expect to be able to publish kit costs by the beginning of April. The initial costs should ramp down as we achieve scale.

Kevin McCarthy