Oxford Nanopore @ ASHG

GW_OK · 11-07-2012, 10:29 AM

New thread started for ONT discussion as the old one was getting long. Also, GridION spotted in the wild?

Quote:

Originally Posted by twitter

Roger Pettett ‏@zerojinx

Guess that ware! #ashg2012 pic.twitter.com/Umfu2chX

So it's not a hollow box...

A call out to all ASHG attendees to please document ONT's announcements and hardware here for the community not attending.

GenoMax · 11-07-2012, 10:42 AM

Is that sequencing cartridge actually connected to the rest of the electronics

Can't really tell from the photo.

GW_OK · 11-07-2012, 11:31 AM

Another twitter pic from Yaniv erlich ‏(@erlichya)
GridIONs in a rack.

GW_OK · 11-07-2012, 12:20 PM

Another twitter pic from Yaniv erlich ‏(@erlichya)
Touching a minION

Info from another person I know attending ASHG:

Quote:

No info on when for sale or price. Essentially error free to 10 kb - not sure I heard that right. No data to release. Just starting early access program.

Nanoporous · 11-07-2012, 12:38 PM

Thanks for the info. Getting the same vibe from following other Twitter accounts - no data yet.

On the other hand, they are doing some cheeky marketing:

(that is the Ion Torrent Bus!) (Photo from: @NeonAardvar on Twitter)

GW_OK · 11-07-2012, 02:25 PM

Quote:

Joshua Randall ‏@joshulux
Single-use MinION from Oxford Nanopore will cost ~$1000 and yield ~10Gbases in 6 hours with reads up to 40kb.

GW_OK · 11-08-2012, 07:18 AM

Yaniv erlich ‏@erlichya
Based on oxford nanopore representative explanations, here is a technical annotation of the MinIon picture #ashg2012

GW_OK · 11-08-2012, 07:25 AM

Einstein Epigenomics Einstein Epigenomics ‏@EpgntxEinstein
Oxford Nanopore powered up #ASHG2012

GW_OK · 11-08-2012, 07:35 AM

Good blog post toning down the hype over at mikethemadbiologist's page

h2so4hurts · 11-08-2012, 07:41 AM

Anyone can put a plexiglass top on a microATX case full of wires...Mike's post reflects my own opinions, I HOPE this isn't all just marketing. But it's really hard to not yell bull**** if they're not going to release data or show these things actually *doing* something.

Nanoporous · 11-08-2012, 09:28 AM

Quote:

"wait for Nanopore’s sequencing data has been like waiting for Godot"

http://blogs.nature.com/news/2012/11...s-meeting.html

h2so4hurts · 11-08-2012, 09:39 AM

Good article

Quote:

Chief Executive Officer Gordon Sanghera spent some time telling me how the technology could tag proteins or microRNA with specially-made DNA strands and be used for detection, but he wouldn’t say a word about the company’s timeline for DNA sequencing. Instead, he urged patience. “What we said at AGBT, we will make good.”

I thought they said beta units would be out by September or October and they'd go on sale in December. It'd be a lot easier to be patient if they spared us the dog and pony show and just delivered.

Scoob · 11-08-2012, 10:01 AM

Hmm. My XBox 360 looks a lot like that.....

ECO · 11-08-2012, 11:58 AM

Overall my conversation was pretty disappointing as far as new info (although the gentleman I talked to resisted a pretty good grilling from me and a 454/Roche product manager).

Points from my conversation that I can remember...

GridION == "4-5x more sensors" than the MinION (no comparative runtime specs).
GridION can sip from a 96 well plate full of samples (this was demo'd as a flat bottom black microtiter plate with no septa...hmmm).
Acquisition speed == "bases per second".
The above picture suggesting sample prep is just a "10bp overhang" is not correct and not confirmed
The prototypes of the MinION ended up much larger than shown at AGBT due to heat issues (had to "add fans").
They will not confirm which gating protein (exo or phi29) or which pore (mspA or a-HL), but that the gate protein is not covalently coupled to the pore. (which strongly suggests to me that it is phi29...the exo-release method would undoubtedly need exquisite positioning for efficient detection)
According to the CEO, the DNA input concentration is "nanomolar". This makes sense to be given the binding kinetics of phi29 to it's binding site...but translates into high concentrations for a single molecule platform. When questioned about the possibility of doing very dilute samples where all the molecules matter, he suggested some method of on-chip enrichment/concentration (?????).
They are cagey about data release because they want to (my paraphasing) "release data when it's ready"

Anyway, that's all I got. The ratio of ([booth girls] + [Apple-esque brushed aluminum] + [blinky lights]) to (data) was undefined...so that seems to speak for itself.

HESmith · 11-08-2012, 12:33 PM

Quote:

Originally Posted by ECO

The ratio of ([booth girls] + [Apple-esque brushed aluminum] + [blinky lights]) to (data) was undefined...

Since data = 0, don't you mean infinite?

scbaker · 11-08-2012, 12:34 PM

Quote:

Originally Posted by ECO

Overall my conversation was pretty disappointing as far as new info (although the gentleman I talked to resisted a pretty good grilling from me and a 454/Roche product manager).

Points from my conversation that I can remember...

GridION == "4-5x more sensors" than the MinION (no comparative runtime specs).
GridION can sip from a 96 well plate full of samples (this was demo'd as a flat bottom black microtiter plate with no septa...hmmm).
Acquisition speed == "bases per second".
The above picture suggesting sample prep is just a "10bp overhang" is not correct and not confirmed
The prototypes of the MinION ended up much larger than shown at AGBT due to heat issues (had to "add fans").
They will not confirm which gating protein (exo or phi29) or which pore (mspA or a-HL), but that the gate protein is not covalently coupled to the pore. (which strongly suggests to me that it is phi29...the exo-release method would undoubtedly need exquisite positioning for efficient detection)
According to the CEO, the DNA input concentration is "nanomolar". This makes sense to be given the binding kinetics of phi29 to it's binding site...but translates into high concentrations for a single molecule platform. When questioned about the possibility of doing very dilute samples where all the molecules matter, he suggested some method of on-chip enrichment/concentration (?????).
They are cagey about data release because they want to (my paraphasing) "release data when it's ready"

Anyway, that's all I got. The ratio of ([booth girls] + [Apple-esque brushed aluminum] + [blinky lights]) to (data) was undefined...so that seems to speak for itself.

Thanks for summarizing for those of us who couldn't be at ASHG. All indications up to now have been for ONT using a highly modified version of a-HL, so I'd be surprised if the first version actually uses mspA. In terms of the exonuclease method, I'm pretty sure it's been abandoned (or put waaaay back on the backburner - hence the 'arbitration hearing' between ONT and Illumina).

ECO · 11-08-2012, 12:56 PM

Quote:

Originally Posted by HESmith

Since data = 0, don't you mean infinite?

If it were approaching zero, it would be approaching infinity. It was zero...and x/0 == undef.

HESmith · 11-08-2012, 12:59 PM

Quote:

Originally Posted by ECO

If it were approaching zero, it would be approaching infinity. It was zero...and x/0 == undef.

Touche! (or, in the immortal words of Buzz Lightyear, "To inifinity and beyond!")

Definitely getting punchy...

Nanoporous · 11-08-2012, 02:21 PM

Quote:

Originally Posted by ECO

Overall my conversation was pretty disappointing as far as new info (although the gentleman I talked to resisted a pretty good grilling from me and a 454/Roche product manager).

Points from my conversation that I can remember...

GridION == "4-5x more sensors" than the MinION (no comparative runtime specs).
GridION can sip from a 96 well plate full of samples (this was demo'd as a flat bottom black microtiter plate with no septa...hmmm).
Acquisition speed == "bases per second".
The above picture suggesting sample prep is just a "10bp overhang" is not correct and not confirmed
The prototypes of the MinION ended up much larger than shown at AGBT due to heat issues (had to "add fans").
They will not confirm which gating protein (exo or phi29) or which pore (mspA or a-HL), but that the gate protein is not covalently coupled to the pore. (which strongly suggests to me that it is phi29...the exo-release method would undoubtedly need exquisite positioning for efficient detection)
According to the CEO, the DNA input concentration is "nanomolar". This makes sense to be given the binding kinetics of phi29 to it's binding site...but translates into high concentrations for a single molecule platform. When questioned about the possibility of doing very dilute samples where all the molecules matter, he suggested some method of on-chip enrichment/concentration (?????).
They are cagey about data release because they want to (my paraphasing) "release data when it's ready"

Anyway, that's all I got. The ratio of ([booth girls] + [Apple-esque brushed aluminum] + [blinky lights]) to (data) was undefined...so that seems to speak for itself.

Thanks for the very nice summary.

For the 'gate' protein, I think they are using some sort of a motor protein to slow down the motion of the DNA in a stepwise manner. As per Clive Brown's talk at AGBT, it is certainly not attached to the pore, and that it is definitely not phi29 (which is what the Akeson and Gundlach groups are using). A polymerase like that would require that you add NTPs. So probably a helicase or something.

TonyBrooks · 11-09-2012, 02:52 AM

Maybe ONT have learnt from PacBio's mistakes. Remember the anticlimax when you first saw PacBio data?

Nanopore error rate is around 4% ~Q14, or at least it was 9 months ago.
The problem is we've all been spoilt by Illumina SBS and will see anything with < Q30 (or even Q20). They've gone on record saying they won't release anything until error is <1% (which is probably nearer the acceptable level). How far away from that they are is anyone's guess at the moment.

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11-07-2012, 12:38 PM	#5
Nanoporous Junior Member Location: San Diego Join Date: Dec 2009 Posts: 7	Thanks for the info. Getting the same vibe from following other Twitter accounts - no data yet. On the other hand, they are doing some cheeky marketing: (that is the Ion Torrent Bus!) (Photo from: @NeonAardvar on Twitter) Last edited by Nanoporous; 11-07-2012 at 12:43 PM.

11-08-2012, 10:01 AM	#13
Scoob Junior Member Location: London Join Date: Feb 2010 Posts: 4	GridIron Hmm. My XBox 360 looks a lot like that.....

11-08-2012, 11:58 AM	#14
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,355	Overall my conversation was pretty disappointing as far as new info (although the gentleman I talked to resisted a pretty good grilling from me and a 454/Roche product manager). Points from my conversation that I can remember... GridION == "4-5x more sensors" than the MinION (no comparative runtime specs). GridION can sip from a 96 well plate full of samples (this was demo'd as a flat bottom black microtiter plate with no septa...hmmm). Acquisition speed == "bases per second". The above picture suggesting sample prep is just a "10bp overhang" is not correct and not confirmed The prototypes of the MinION ended up much larger than shown at AGBT due to heat issues (had to "add fans"). They will not confirm which gating protein (exo or phi29) or which pore (mspA or a-HL), but that the gate protein is not covalently coupled to the pore. (which strongly suggests to me that it is phi29...the exo-release method would undoubtedly need exquisite positioning for efficient detection) According to the CEO, the DNA input concentration is "nanomolar". This makes sense to be given the binding kinetics of phi29 to it's binding site...but translates into high concentrations for a single molecule platform. When questioned about the possibility of doing very dilute samples where all the molecules matter, he suggested some method of on-chip enrichment/concentration (?????). They are cagey about data release because they want to (my paraphasing) "release data when it's ready" Anyway, that's all I got. The ratio of ([booth girls] + [Apple-esque brushed aluminum] + [blinky lights]) to (data) was undefined...so that seems to speak for itself.

11-07-2012, 10:42 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,854	Is that sequencing cartridge actually connected to the rest of the electronics Can't really tell from the photo.

11-07-2012, 11:31 AM	#3
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 408	Another twitter pic from Yaniv erlich ‏(@erlichya) GridIONs in a rack.

11-08-2012, 07:18 AM	#7
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 408	Yaniv erlich ‏@erlichya Based on oxford nanopore representative explanations, here is a technical annotation of the MinIon picture #ashg2012

11-08-2012, 07:25 AM	#8
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 408	Einstein Epigenomics Einstein Epigenomics ‏@EpgntxEinstein Oxford Nanopore powered up #ASHG2012

11-08-2012, 07:35 AM	#9
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 408	Good blog post toning down the hype over at mikethemadbiologist's page

11-08-2012, 07:41 AM	#10
h2so4hurts Junior Member Location: Gainesville, FL Join Date: Jan 2010 Posts: 3	Anyone can put a plexiglass top on a microATX case full of wires...Mike's post reflects my own opinions, I HOPE this isn't all just marketing. But it's really hard to not yell bull**** if they're not going to release data or show these things actually doing something.

11-09-2012, 02:52 AM	#20
TonyBrooks Senior Member Location: London Join Date: Jun 2009 Posts: 298	Maybe ONT have learnt from PacBio's mistakes. Remember the anticlimax when you first saw PacBio data? Nanopore error rate is around 4% ~Q14, or at least it was 9 months ago. The problem is we've all been spoilt by Illumina SBS and will see anything with < Q30 (or even Q20). They've gone on record saying they won't release anything until error is <1% (which is probably nearer the acceptable level). How far away from that they are is anyone's guess at the moment.