[Jon_Keats]

I'm betting PGM will still have a place in the clinic, there just are not that many clinically relevant things to screen for on a mass scale. Though for some clinical assays like MRD assays or gene expression a bit higher read count would be nice and it is scary to hear that the PGM may be limited to around 10M sensors when the 318 is at 12M... sounds like a 320 chip is not coming... Argh
Now I'm hoping our 4 PGM order didn't go out the door, what did Nick call it... The Osborne Effect

[singaporeseq]

So I guess it's the end of the scalability claim for PGM...unless you want to pay 200K for a Ion Proton....I don't imagine we'll be seeing a 320 chip ...

[BBoy]

Sorry to be pedantic, but the chip in the image clearly isn't square (measures up using the high tech method of "ruler against screen" with edge ratio of 2x1.6) that aside, back to the sensor size (I won't use "pixels" to describe them again, perhaps they should be called sexels (sensor elements)).

Have just been back and reworked (post coffee) some of the sensor dimensions. Using images of sensor cross-section posted previously here, the sensors on the 318 chip are ~4.1um edge-to-edge, with ~3.4 um diameter wells, and ~0.7um well to well spacing.

For Proton I, the sensor size (at ~170M per chip) must be ~2um2. Assuming a square sensor (not necessarily a good approximation, but let's go with it for now), the sensor width would be ~1.4um. If the ratio of well width to sensor spacing is preserved relative to the 318 chip, then the well would be ~1.16um wide, and the intersensor spacing would be ~0.25 um.

For Proton II, the sensor size (at ~660M per chip) must be ~0.5um2. Assuming a square sensor (still probably not the best approximation...), the sensor width would be ~0.7um. If the ratio of well width to sensor spacing is preserved relative to the 318 chip, then the well would be 0.58um wide, and the intersensor spacing would be 0.125 um.

This all assumes that there will be no increase in cross-talk between wells or sensors as the density increases.

Even with this best case scenario, the well width on the Proton II will be ~0.6um, which would require the use of 0.2-0.3um diameter beads. Perhaps that isn't so unreasonable?

4x increase in sensel count without an increase in die size in under a year (if the current propaganda is to be believed) does not sound very plausible. Having said that, it is not completely out of the realm of possibility.

Perhaps given Ion's published sensor response (mV/pH, somewhere in their Nature paper if I recall correctly) can someone back-calculate a lower limit on the bead size? You need to generate enough protons at each flush cycle to to swing the pH by a measurable amount (a few mV, I would imagine).

[DICER]

Another pic of chip...


<snip>

Can anyone read or figure out the coding tag of the chip? Is that already P 6 or are my eyes playing up?

BTW is there going to be special centrifuges?

Pixel, Sensel, Hexel, Hexwels....

H+ e- X el-ectronics

[tlking]

I am interested to know how Ion Torrent PGM customers feel about this news...

As an owner of an Ion Torrent PGM, I am excited to know that Life Tech has put resources into expanding the technology. We are very pleased with the output from our PGM and OneTouch.

[ymc]

If ion can do a 30x genome in 3 hours, doesn't that mean their throughput is higher than HiSeq 2500 by 7x???

[epistatic]

With that many wells, how many beads will you need to input into the emulsions? My rep said it requires a new one-touch, I wonder if they will have to move to bag emPCR and use the SOLiD's EZ bead system to make that many beads. Input beads * 8-10% enriched = >165-660M beads to load onto the chip? That will be a lot of Taq. I wonder what sample prep will add to the $1K price.

Speed of getting that much data will be quite useful, hope the prep has similar improvements.

[hamiguo]

avarage RL 390bp，longest 700bp， i’ve seen this file

[gringer]

Pixel, Sensel, Hexel, Hexwels....

Sensel and photosites are used in digital cameras:

http://en.wikipedia.org/wiki/Pixel

http://www.cambridgeincolour.com/tutorials/camera-sensors.htm

Other possible words playing on these names: hydrosites, protosites, ionocells, ionosites

[aleferna]

No wonder Life are selling the original PGM's off at a dirt cheap price.

Says who, we just got a tender for a PGM last week... seems price discounts do not come to Europe that easily...

[aleferna]

Question, how do you fragment the library, are you using sonication or the IonShear. We are trying to buy a MiSeq/PGM but we can use Nextera with the MiSeq, with the PGM do you need a sonicator? I mean requiring a Covaris would certainly put the PGM out of our reach...

[DICER]

Sensel and photosites are used in digital cameras:

http://en.wikipedia.org/wiki/Pixel

http://www.cambridgeincolour.com/tutorials/camera-sensors.htm

Other possible words playing on these names: hydrosites, protosites, ionocells, ionosites

protoxels, protonels...

perhaps the Ion One Touch disappears in October?

[nickloman]

They announced a OneTouch for Proton.

[nickloman]

Ion Torrent are keen to point out that PGM users (current or prospective) will get a decent discount on the Proton (nearly the entire cost of the PGM) if they "upgrade", plus they get to keep their PGM. Which seems like a fair deal.

[epistatic]

The Ion Proton Sequencer, $149,000
Ion Proton OneTouch and Proton Server, $95,000
Service Contract (per year), $30,000 (rep estimate, first year free)
Total Five Year Investment, $364,000


The cost isn't as low as the PGM but the most impressive part is the $1K all inclusive sequencing price. I thought the $1K was just the price for the chip and the sequencing reagents, our rep says it includes everything from Ion to do DNA -> library -> emPCR -> sequencing -> fastq if doing a standard shotgun prep. It is fair that an RNA kit or capture kit would cost more.

$1,000 run price "does include library (if fragment) prep, template prep, sequencing consumables and reagents (pretty much everything except basic lab supplies)"

Now how to figure out what mark up will be needed to pay the service contract and staff to run it.