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-   -   Oxford Nanopore @ ASHG (http://seqanswers.com/forums/showthread.php?t=24807)

GW_OK 11-07-2012 09:29 AM

Oxford Nanopore @ ASHG
 
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

https://pbs.twimg.com/media/A7Hgn6PCUAAkfec.jpg


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 09:42 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 10:31 AM

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

https://pbs.twimg.com/media/A7HwAIACAAAHQJd.jpg

GW_OK 11-07-2012 11:20 AM

Another twitter pic from Yaniv erlich ‏(@erlichya)
Touching a minION
https://pbs.twimg.com/media/A7H9NQuCcAAnB2t.jpg


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 11:38 AM

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:

https://pbs.twimg.com/media/A7DrRXqCYAA0xHm.jpg:large
(that is the Ion Torrent Bus!) (Photo from: @NeonAardvar on Twitter)

GW_OK 11-07-2012 01:25 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.
https://pbs.twimg.com/media/A7IaxIdCUAA6EYS.jpg

GW_OK 11-08-2012 06:18 AM

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

https://pbs.twimg.com/media/A7L_-PxCQAAOAuK.png

GW_OK 11-08-2012 06:25 AM

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

https://pbs.twimg.com/media/A7I6mmNCAAAnj_e.jpg

GW_OK 11-08-2012 06:35 AM

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

h2so4hurts 11-08-2012 06:41 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 08:28 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 08:39 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 09:01 AM

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

ECO 11-08-2012 10:58 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 11:33 AM

Quote:

Originally Posted by ECO (Post 88859)
The ratio of ([booth girls] + [Apple-esque brushed aluminum] + [blinky lights]) to (data) was undefined...

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

scbaker 11-08-2012 11:34 AM

Quote:

Originally Posted by ECO (Post 88859)
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 11:56 AM

Quote:

Originally Posted by HESmith (Post 88864)
Since data = 0, don't you mean infinite? :rolleyes:

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

HESmith 11-08-2012 11:59 AM

Quote:

Originally Posted by ECO (Post 88866)
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 01:21 PM

Quote:

Originally Posted by ECO (Post 88859)
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 01:52 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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