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Old 01-10-2012, 08:53 AM   #21
ECO
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JP Morgan conference at 9am PST will most likely bring Illumina's response!
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Old 01-10-2012, 08:58 AM   #22
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JP Morgan conference at 9am PST will most likely bring Illumina's response!
Yep, I'm following #JPM12 and keen to see what is said! I was kind of expecting platform announcements to be made at AGBT but seems that's too far away for $ILMN and $LIFE.
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Old 01-10-2012, 09:14 AM   #23
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Right now they haven't got anything as this is just an announcement... first machines to early access customers mid-2012.
They've got something or they wouldn't be announcing it. Then again, they did promise quite a bit more than the ion torrent turned out to be.. We'll see what's hype and what isn't.

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Strongly expect to see Illumina announcements reacting to this!
Indeed. Anyone see the latest bit from nanopore in last months Nature Nanotechnology? Looks promising...

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We don't really know!
Then I won't get excited about it....
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Old 01-10-2012, 09:14 AM   #24
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Woosh, here goes!

Illumina announces #HiSeq 2500: able to seq entire genome or 20 exomes in 24h. #JPM12 #GenomeInADay
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Old 01-10-2012, 09:18 AM   #25
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Man, where can I watch this thing?
Also, chemistry? Tech? What's the new sauce?
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Old 01-10-2012, 12:05 PM   #26
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BTW I would think the chip is more like 20mm^2 (old chips 9mm^2) and they will be working on near-complete loading.
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?
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Old 01-10-2012, 01:15 PM   #27
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Here's the announcement from Illumina about the HiSeq 2500 "genome-in-a-day" machine http://investor.illumina.com/phoenix...757&highlight=
We should talk about Illumina stuff in the Illumina forum:
http://seqanswers.com/forums/showthread.php?t=16725
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Old 01-10-2012, 01:23 PM   #28
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Yeah I wouldn't be very happy unboxing a new instrument with a planned obsolescence date of mid-2012.
I don't see this as making the PGM obsolete. PGM will come in at a lower price point; with all the accessories the all-in price of a PGM is going to be about 30-40% of the all-in price of the Proton. For a lot of applications, PGM will be sufficient for many researchers.
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Old 01-10-2012, 01:35 PM   #29
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We should talk about Illumina stuff in the Illumina forum:
http://seqanswers.com/forums/showthread.php?t=16725
Thanks, moved them there.
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Old 01-10-2012, 01:47 PM   #30
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Someone just sent me this, claiming it was from their sales rep. Read with caution

Quote:
Hello,
Today Life Technologies has announced the Ion Proton Sequencing Platform-the first benchtop sequencing system capable of completely sequencing an human genome for $1000 in one day. Many more details to come through the day but a few details to take note of below:

Instrument Price: $149,000 (as a current PGM or SOLiD 5500xl owner you can purchase one for $99,000 through the end of the year)
Ancillary Items for Proton (Ion Proton OneTouch and Proton Torrent Server): Pricing not finalized but expected to be $95,000 or less

Chips:

Ion Proton I chip: 165 million wells, run 2 full exomes per chip for $1000
Ion Proton II chip: 660 million wells, run full human genome for $1000 (available towards the end of 2012)
Also deep whole transcriptome analysis can be performed using either chip

Proton Torrent Server-designed to analyzed a human genome without additional servers in one day providing primary and secondary analysis

More details to follow in the next couple of days!

Also a number of additional updates to the PGM platform were announced yesterday-please take a look below and let me know if you have any questions! Look to the Ion Community for additional information also.

Sequencing chips:

318 chip (1Gb) now officially released in 4 and 8 packs. Cost per chip is $500/chip
316 chip-cost reduced from $500 to $299/chip. This will reduce your 316 complete run cost by ~ 40%

Template prep and sequencing kits:

Updated 200bp Template prep kits for both manual and OneTouch applications, sequencing kits with improved accuracy for more throughput. For use with all size chips.
Release of Ion-demonstrated protocols for 2 x 100bp paired end sequencing
Barcode kits availability increased from 16 to 32. Additional barcode options on Ion Community site up to 96 now available

AmpliSeq Updates:

Launch of Ion AmpliSeq Designer for custom AmpliSeq Panels in March. Rapid 48hr design turnaround, 2-4 week assay delivery. Up to 1536 targets in a single tube
AmpliSeq Comprehensive Cancer Panel-targets over 400 genes involved in tumor formation with 95% of targets at 500X coverage using 318 chip. Early access in Q1, full release in Q2 2012. Detailed gene list on Ion Community
AmpliSeq Inherited Disease Gene Panel targeting genes implicated in over 140 inherited diseases (300 genes, 10,000 amplicons) at ~30X coverage using the 316 chip. Early access in Q1, full release in Q2 2012. Detailed gene list on Ion Community
Protocols for barcoding of all Ion AmpliSeq custom or fixed panels available. Can do up to 4 Cancer Panel barcoded samples on a 316 chip or 6 normal/tumor pairs on the 318 chip.
New website available for designs: www.ampliseq.com

Torrent Suite and Software:

Version 2.0 includes updates for 318 chip, new unified variant caller to combine germline and AmpliSeq callers. Enhancements to algorithms, basecalling time (30% faster), increased INDEL calling, work with any reference
Launch of Torrent Circuit-central repository for download of analysis plug-ins for Torrent Suite from both Ion Torrent developers and Ion Community contributers
Early Access Launch of Ion Reporter-secure hosted data analysis using cloud structure. Enables simplified routine data analysis for AmpliSeq projects

RNA Seq:
Coming soon-white paper and application note describing comparison of RNA Seq on Ion Torrent to microarrays and qPCR
RNA How to Guide for application development, protocols, FAQ’s, etc

Misc upgrades and enhancements:

Announcing New England Biolabs NEBnext Fast Library Construction Kits-2hr protocol (12 min hands on time) for libraries up to 300bp in size
Availability of ELGA PURELAB flex water Purification System-simple to set up ultrapure water source and validated with the Ion PGM System
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Old 01-10-2012, 09:42 PM   #31
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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
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Old 01-10-2012, 10:15 PM   #32
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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 ...
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Old 01-10-2012, 11:09 PM   #33
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Originally Posted by 454newbie View Post
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).
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Old 01-11-2012, 04:28 AM   #34
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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

Last edited by DICER; 01-11-2012 at 04:31 AM.
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Old 01-11-2012, 07:18 AM   #35
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Originally Posted by nickloman View Post
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.
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Old 01-12-2012, 12:07 AM   #36
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If ion can do a 30x genome in 3 hours, doesn't that mean their throughput is higher than HiSeq 2500 by 7x???
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Old 01-12-2012, 03:55 PM   #37
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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.
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Old 01-12-2012, 06:18 PM   #38
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avarage RL 390bp,longest 700bp, iíve seen this file
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Old 01-13-2012, 01:41 AM   #39
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Quote:
Pixel, Sensel, Hexel, Hexwels....
Sensel and photosites are used in digital cameras:

http://en.wikipedia.org/wiki/Pixel
http://www.cambridgeincolour.com/tut...ra-sensors.htm

Other possible words playing on these names: hydrosites, protosites, ionocells, ionosites
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Old 01-13-2012, 02:46 AM   #40
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Originally Posted by TonyBrooks View Post
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...
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