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

GW_OK 11-07-2012 10:29 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 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.

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

GW_OK 11-07-2012 12:20 PM

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 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:

https://pbs.twimg.com/media/A7DrRXqCYAA0xHm.jpg:large
(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.
https://pbs.twimg.com/media/A7IaxIdCUAA6EYS.jpg

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

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

GW_OK 11-08-2012 07:25 AM

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

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

GW_OK 11-08-2012 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

GridIron
 
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 (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 12:34 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 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 (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 12:59 PM

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 02:21 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 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.

GenoMax 11-09-2012 04:49 AM

Quote:

Originally Posted by TonyBrooks (Post 88923)
Maybe ONT have learnt from PacBio's mistakes. Remember the anticlimax when you first saw PacBio data?

There is some truth to that. Unfortunately this is starting to feel like "Duke Nukem Forever".

GW_OK 11-09-2012 07:54 AM

I think they could release something and just put a giant red asterisk next to it saying this is only really, really preliminary data, really.

Any data at all would, I think, get people to cut them some slack.

earonesty 11-09-2012 09:56 AM

Quote:

Originally Posted by TonyBrooks (Post 88923)
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.

PacBio reads, at Q8, are still quite useful for scaffolding assemblies. Crazy to hold back data when there are lots of people who could make use of long Q14 reads right now.

BadDNA 11-09-2012 11:49 AM

Let us scaffold!
 
Quote:

Originally Posted by earonesty (Post 88978)
PacBio reads, at Q8, are still quite useful for scaffolding assemblies. Crazy to hold back data when there are lots of people who could make use of long Q14 reads right now.

I agree completely!

DaleYuzuki 11-10-2012 06:18 AM

If anyone's interested, I wrote up this post after talking with Oxford and several others at ASHG.

Really too bad that there wasn't any firm specifications or pricing.

Dale

TonyBrooks 11-12-2012 06:49 AM

Quote:

Originally Posted by earonesty (Post 88978)
PacBio reads, at Q8, are still quite useful for scaffolding assemblies. Crazy to hold back data when there are lots of people who could make use of long Q14 reads right now.

The problem is that scaffold runs for de novo are so niche in the grand scheme of things. The real money will be in resequencing, RNA-Seq, ChIP-Seq etc. As a core group, I'd say 99% of things we get asked to do fall into those categories. There's still a long way to go for ONT until it becomes a viable alternative.
Q14 is only really of value when you have a bunch of short read Q30s you can pin to the scaffold.

ECO 11-12-2012 11:22 PM

Quote:

Originally Posted by DaleYuzuki (Post 89027)
If anyone's interested, I wrote up this post after talking with Oxford and several others at ASHG.

Really too bad that there wasn't any firm specifications or pricing.

Dale

That ONT post mentioned Ion Torrent's party more than it did ONT. Heh.

GW_OK 11-13-2012 06:59 AM

Dale's post does have an insightful comment at the bottom. How much of the silence from ONT is because they don't have anything to show and how much is due to their current arbitration with Illumina? Maybe they're just playing it close to the vest?

seqnextgen 11-13-2012 10:04 PM

Quote:

Originally Posted by TonyBrooks (Post 89086)
The problem is that scaffold runs for de novo are so niche in the grand scheme of things. The real money will be in resequencing, RNA-Seq, ChIP-Seq etc. As a core group, I'd say 99% of things we get asked to do fall into those categories. There's still a long way to go for ONT until it becomes a viable alternative.
Q14 is only really of value when you have a bunch of short read Q30s you can pin to the scaffold.

Maybe, but once de novo assembly is really available with a reasonable price, I believe it is the way to go. Ever wonder where those "copy number variants" are in a genome. It might be hard to believe that where they are is not important.

pmiguel 11-14-2012 04:43 AM

The other major claim is that no library construction (or even DNA purification) is required. That would immediately put these devices in their own league. That makes HiSeqs and Torrents niche instruments.

Of course there is the weaselly "sample needs 10 base single stranded leader" statement. Not sure what that means. Like you need a cos site digested with lambda terminase? Or you can just heat your sample a little to melt the terminii?

--
Phillip

seqnextgen 11-14-2012 06:36 AM

Quote:

Originally Posted by pmiguel (Post 89217)
The other major claim is that no library construction (or even DNA purification) is required. That would immediately put these devices in their own league. That makes HiSeqs and Torrents niche instruments.

....

--
Phillip

I think ECO can probably comment on this better. All I know is once you go to single molecule world, any impurity can kill the sequencing mechanism / basecalling accuracy easily. Any "single molecule" impurities including any ion that one does not anticipate during engineering phase is the enemy, so, good luck for the "no sample preparation" claim. (Not saying it can not be simple, but sequencing DNA in blood with zero sample-prep to get high throughput results? one can judge that with common sense...)

Amiga 11-15-2012 06:32 PM

The grand scheme of things of for-profit sector is targeted resequencing for diagnostic. The only thing ONT are proposing that could be useful to them is the no sample prep at all. And I am having a hard time believing that.

While a $100 disposable cartridge would be nice too, especially to forensic and DTC providers, a Q14 isn't useful for any of them.

I agree with other people prediction that ONT will be the next PacBio. It's noble to claim that they will delay their launch until they get Q30, but they need investors, and the current ones will eventually want to cash in. PacBio was able to hype and overhype for 5 years. How much longer is it going to be for ONT?

seqnextgen 11-15-2012 11:10 PM

Just a quick reminder of some facts. For ONT to be next PacBio, at least they need to show some data and publish papers in NEJM from sample to print within weeks, not once, but twice. And, they will also need to publish DNA sequencing data/DNA modification data in Nature / Nature Biotech to show important biological results that can not be resolved by 2nd gen. sequencing / Sanger sequencing, etc. (Not just nucleotide identification. DNA sequencing is not about identifying bases/short segments. DNA sequencing should be about efficiently linking long range information...) Commercially successfully or not, the publications and real data already help to reveal some new biology. Until nanopore is no longer nanovapor, there is no fair comparison.

BBoy 02-15-2013 01:30 AM

Quote:

Originally Posted by seqnextgen (Post 89400)
Just a quick reminder of some facts. For ONT to be next PacBio, at least they need to show some data and publish papers in NEJM from sample to print within weeks, not once, but twice. And, they will also need to publish DNA sequencing data/DNA modification data in Nature / Nature Biotech to show important biological results that can not be resolved by 2nd gen. sequencing / Sanger sequencing, etc. (Not just nucleotide identification. DNA sequencing is not about identifying bases/short segments. DNA sequencing should be about efficiently linking long range information...) Commercially successfully or not, the publications and real data already help to reveal some new biology. Until nanopore is no longer nanovapor, there is no fair comparison.

Well said...

paulk 02-15-2013 06:47 PM

Quote:

Originally Posted by TonyBrooks (Post 89086)
The problem is that scaffold runs for de novo are so niche in the grand scheme of things.

Not really; I'd love to be able to quickly map out cancer genome rearrangements and a 4% error rate wouldn't bother me for that purpose.

I wonder what updates will come out next week at AGBT...

seqnextgen 03-03-2013 11:00 AM

Quote:

Originally Posted by paulk (Post 96576)
Not really; I'd love to be able to quickly map out cancer genome rearrangements and a 4% error rate wouldn't bother me for that purpose.

I wonder what updates will come out next week at AGBT...

AFAIK, nothing..... no data, no status update, not even a cool USB sequencer full with data found in a bar

krobison 03-04-2013 05:49 AM

Quote:

Originally Posted by seqnextgen (Post 98034)
AFAIK, nothing..... no data, no status update, not even a cool USB sequencer full with data found in a bar

What? You weren't out on the strand digging through sand like a madman? :)

BBoy 03-04-2013 10:39 PM

Quote:

Originally Posted by krobison (Post 98066)

Apparently we have all been asleep at the wheel. The minion has been out for decades, the first model has even made it to a museum:
http://core-genomics.blogspot.com/20...announced.html

GW_OK 03-06-2013 07:47 AM

Quote:

Originally Posted by krobison (Post 98066)

I confess that I did stroll through the beach area around the suites (on my way to my next meeting! I was going through there anyway, honest!) looking for disturbed sand patches.

I should have been stalking the bar, apparently.

seqnextgen 03-06-2013 07:47 AM

Quote:

Originally Posted by krobison (Post 98066)

I thought it was a joke originally, obviously, pathogenomics did find a MiniIon in AGBT. This is probably more comprehensive non-update one can find now
http://pathogenomics.bham.ac.uk/blog...-at-agbt-2013/

Jeremy 03-06-2013 05:38 PM

Quote:

Originally Posted by Clive
([url
http://pathogenomics.bham.ac.uk/blog/2013/03/a-chat-with-oxford-nanopores-clive-brown-at-agbt-2013[/url])
“We didn’t even know that long reads were so important to people until after that AGBT presentation.”

Really? I find that hard to believe.

ECO 03-07-2013 10:42 AM

Waaaaaa we made promises we couldn't keep to get attention and funding...and now people expect us to keep them!

<tiny violin playing>

Seriously though, having been through the bring up of a single molecule sequencer...if the CTO is opining in a bar to a blogger about improving consensus accuracy by throwing in multiple types of pores...they are a LONG way from finalizing a chemistry, let alone stabilizing and commercializing it.

Happy to eat words. Actually I love having my pessimism proven wrong.

And I hope I'm not off Clive's list. I could do some long range clinical haplotyping pretty easily! ;)

GenoMax 03-07-2013 10:49 AM

Quote:

Originally Posted by ECO (Post 98510)
And I hope I'm not off Clive's list.

Perhaps not before this post.

But now you can't be sure :D

nickloman 03-07-2013 11:16 AM

Quote:

Originally Posted by ECO (Post 98510)
Seriously though, having been through the bring up of a single molecule sequencer...if the CTO is opining in a bar to a blogger about improving consensus accuracy by throwing in multiple types of pores...they are a LONG way from finalizing a chemistry, let alone stabilizing and commercializing it.

Just to note I added a clarification from Clive at the bottom of the post on that particular point...

Given that they are continuously screening new and better pores and that is in fact one of the cool things about a biological nanopore (just like other sequencing companies regularly screen for new polymerases), I didn't necessarily see that as reflective of where they are in the product development pipeline.

GenoMax 03-07-2013 11:31 AM

Quote:

Originally Posted by nickloman (Post 98517)
Given that they are continuously screening new and better pores and that is in fact one of the cool things about a biological nanopore (just like other sequencing companies regularly screen for new polymerases), I didn't necessarily see that as reflective of where they are in the product development pipeline.

No argument there.

We all hope they will stop the screening at some point and release the first product we can use.

GW_OK 10-18-2013 10:25 AM

So.
ASHG next week.
Any care to give odds on ONT:
A) Being present?
B) Announcing anything? (Announcing no announcements does not count)

To aid in your handicapping, a certain Clive Brown tweeted:
Quote:

Clive G. Brown ‏@Clive_G_Brown 9 Oct

I've reluctantly rejoined twitter purely so that I can make one tweet - when the appropriate time arises ...
Also, it appears the Minion is now sporting a new look.

GenoMax 10-18-2013 10:31 AM

Hopefully they are not going to wait till illumina's "right to negotiate" expire at end of 2016?

bstamps 10-18-2013 11:37 AM

I'm guessing


A) 100%
B) 75/25. Either they release something, or risk losing funding from investors at this point. My bet is that they release the Minion sooner than the Gridion.

GenoMax 10-18-2013 11:44 AM

Quote:

Originally Posted by bstamps (Post 119265)
I'm guessing


Either they release something, or risk losing funding from investors at this point. My bet is that they release the Minion sooner than the Gridion.

They just raised $64 Million this month: http://nextgenseek.com/2013/10/oxfor...es-64-million/ Clearly investors must have seen something that we do not have access to (yet).

BBoy 10-19-2013 12:50 AM

Quote:

Originally Posted by GenoMax (Post 119267)
They just raised $64 Million this month: http://nextgenseek.com/2013/10/oxfor...es-64-million/ Clearly investors must have seen something that we do not have access to (yet).

Maybe they were shown the foils from AGBT 2011 :-)

NextGenSeq 10-21-2013 11:58 AM

You could check their website.

https://www.nanoporetech.com/news/events
ASHG 2013. Oxford Nanopore will be exhibiting at ASHG 2013 in Boston, 22-26 October. http://www.ashg.org/2013meeting/

BBoy 10-21-2013 11:27 PM

Quote:

Originally Posted by NextGenSeq (Post 119475)
You could check their website.

https://www.nanoporetech.com/news/events
ASHG 2013. Oxford Nanopore will be exhibiting at ASHG 2013 in Boston, 22-26 October. http://www.ashg.org/2013meeting/

Hopefully more than mockups with plexiglass cutouts like last time around? Unless they show something this will start turning into the mother of all vaporware. Given that there are no leaks (and there were leaks before AGBT 2012) I am not too hopeful. Will be glad to eat my words.

gringer 10-22-2013 06:33 AM

Apparently position 654 in the exhibition centre at ASHG 2013:

http://www.ashg.org/cgi-bin/2013/ashg13fp.pl

[top left]

GW_OK 10-22-2013 10:10 AM

ONT put up some new movies in the past 4 days. New looks at the GridION cartridge as well as miRNA sequencing and protein detection.

DaleYuzuki 10-22-2013 02:25 PM

Oxford Nanopore at ASHG
 
1 Attachment(s)
Here at the ASHG tradeshow floor setup, was able to spot the Oxford booth. (Attached is a photo, and you can spot the stack of GridIONs on top of the table there.)

I heard a rumor yesterday about them but won't engage in any rumor-mongering. :)

Fred 10-23-2013 05:08 AM

Hi,

Why not try it ?

https://www.nanoporetech.com/technol...cess-programme

Fred

GW_OK 10-23-2013 07:41 AM

ONT is the Kool-aid Man busting through the wall:
"OH YEAH!"

PacBio shares already down 15%.
Some extra info at the bottom of the GenomeWeb article

The MinIons also appear to be re-usable! So, so cool.

GenoMax 10-23-2013 07:56 AM

Quote:

Originally Posted by GW_OK (Post 119711)
The MinIons also appear to be re-usable! So, so cool.

You have to send the MinIons in for recycle/reuse, if I remember correctly.

The article you linked says "participants can order additional flow cells for $999 a piece". I hope that is just during the trial and that the final cost will not be that high.

It would be difficult to keep tens on hand if they are going to cost $1K each.

rahulvrane 10-23-2013 07:56 AM

Maybe I am a bit new to the whole ONT discussion.. But from my read of the website, I see they talk about a 'Run till you get sufficient data' workflow. (Kinda enticing :D )

But has there been any mention of just how long each of these can be run and what the final pore density would be per chip for GridION and MinION?

Obviously the GridION would be a legit superior, but just how far behind is the MinION in performance (or throughput)? ... Any clues I might have missed so far or new ones from the latest ASHG?

Cheers!

GW_OK 10-23-2013 08:20 AM

Quote:

Originally Posted by GenoMax (Post 119712)
You have to send the MinIons in for recycle/reuse, if I remember correctly.

At the beginning of the article they mention the "flow cells" and "usb device" as being separate entities. Also, on the ONT website, they say you can dry down the flowcells before you send them back, a condition of the early access program. This, to me, seems as though the MinIon can accept single use cartridges.

GenoMax 10-23-2013 08:33 AM

Quote:

Originally Posted by GW_OK (Post 119714)
At the beginning of the article they mention the "flow cells" and "usb device" as being separate entities. Also, on the ONT website, they say you can dry down the flowcells before you send them back, a condition of the early access program. This, to me, seems as though the MinIon can accept single use cartridges.

Ah this may is the part that has taken them long to optimize.

It would make sense if the USB device (MinIon) was $1K and the "flowcells" were priced separately, dare we expect "reasonably".

GW_OK 10-23-2013 09:23 AM

Colleagues attending ASHG asked some questions for me. Here's the answers they got:
1) How many pores/average read lengths/flowcell lifespan hours can one expect in the early access Minions?
No info on pore number, they are no reporting it. Read length 5-15kb, lifespan 6-8 hrs. Accuracy depends on speed of reading.

2) What's the shelf life of a Minion flow cell?
Could not report to me a shelf life.

3) Can Minions be used for multiple samples like a Gridion cassette?
Single use only.

rahulvrane 10-23-2013 09:55 AM

Thanks a lot for that GW_OK! :)

I guess the only way the minions are winning is if they can extend the lifespan of the flowcells.

GW_OK 10-23-2013 10:58 AM

Quote:

Originally Posted by GenoMax (Post 119716)
It would make sense if the USB device (MinIon) was $1K and the "flowcells" were priced separately, dare we expect "reasonably".

I have a feeling this is going to be a razor blade marketing strategy. They mention the "flow cells" as being $999. I'll bet you get the Minion free with your first purchase, then you pay for the $1k flowcell every time you want to run it.

Actually, on even further reading, I bet you pay $1k refundable deposit on the device, then $1k for every run on said device, and you can get your deposit back on return of the device.

Of course this is all speculation at the moment and based solely on interpreting the press release of a very secretive company.

GW_OK 10-23-2013 02:57 PM

Go read this about library preps and some nice pics of the minion.

genlyai 11-04-2013 03:29 PM

Quote:

Originally Posted by GW_OK (Post 119720)
Colleagues attending ASHG asked some questions for me. Here's the answers they got:
1) How many pores/average read lengths/flowcell lifespan hours can one expect in the early access Minions?
No info on pore number, they are no reporting it. Read length 5-15kb, lifespan 6-8 hrs. Accuracy depends on speed of reading.

2) What's the shelf life of a Minion flow cell?
Could not report to me a shelf life.

3) Can Minions be used for multiple samples like a Gridion cassette?
Single use only.

I visited their booth and got slightly different info for point 1:

- lifespan 20hrs
- expect 400 functioning pores per minion cell
- speed/accuracy is indeed dialable, with speeds between 10bp/sec and 100bp/sec

Again, this is all by recollection alone (so may be wrong), but I thought it might be of interest. Is anyone in the early access program?

GW_OK 11-05-2013 06:43 AM

Quote:

Originally Posted by genlyai (Post 120750)
Is anyone in the early access program?

Quote:

Originally Posted by twitter
Karen James @kejames
@SFriedScientist I learned a little more about @nanopore’s MinION today from someone at @jacksonlab who is going to get early access. Squee.

I'm guessing the fix is in for a number of early access people, most likely those 40-ish who got to actually see one running at ASHG, plus a few other of the twitterati who seem to know things before most.

ymc 01-16-2014 01:39 PM

Now HiSeqX is announced. Can Girdion compete based on its paper spec announced so far?

gringer 01-16-2014 02:07 PM

It can certainly compete on equipment cost and minimum run cost. ONP has previously claimed that GridION will have sub-$1000 genome sequencing (and not just for human), so I'm guessing yes.

ymc 01-16-2014 04:59 PM

Quote:

Originally Posted by gringer (Post 129858)
It can certainly compete on equipment cost and minimum run cost. ONP has previously claimed that GridION will have sub-$1000 genome sequencing (and not just for human), so I'm guessing yes.

Google tells me even for GridION 8000, their reagent cost is $20-30/Gb.

But HiSeqX is $800/90 = $8.89/Gb:eek:

Certainly their $30K for the box claim can make up a lot of ground

BBoy 01-17-2014 12:05 AM

Quote:

Originally Posted by ymc (Post 129871)
Google tells me even for GridION 8000, their reagent cost is $20-30/Gb.

But HiSeqX is $800/90 = $8.89/Gb:eek:

Certainly their $30K for the box claim can make up a lot of ground

There was a per-Gb cost estimate for the minion that somebody posted, I just can't find it right now. It was ~10x that of a Hiseq and ~2-3x that of Pacbio, sample prep and reagents not included. That was based on the stated flowcell price of $1k and a run time of about 6 hrs, which is the only hard information available about ONT to the general public. There has been zero talk about the gridion even from ONT, so I don't know how their previous claims can be taken as anything more than a marketing spiel.

Let's give them time to actually show that they can sequence and then speculate how they will take over the world. When expectations meet reality, it is usually the latter that retains its reputation. If their early access program is for real some actual information should start coming out this year... unless the fine print at the bottom of the early access application reads "please allow 3-5 years for processing"

ymc 01-17-2014 12:42 AM

Quote:

Originally Posted by BBoy (Post 129900)
There was a per-Gb cost estimate for the minion that somebody posted, I just can't find it right now. It was ~10x that of a Hiseq and ~2-3x that of Pacbio, sample prep and reagents not included. That was based on the stated flowcell price of $1k and a run time of about 6 hrs, which is the only hard information available about ONT to the general public. There has been zero talk about the gridion even from ONT, so I don't know how their previous claims can be taken as anything more than a marketing spiel.

Let's give them time to actually show that they can sequence and then speculate how they will take over the world. When expectations meet reality, it is usually the latter that retains its reputation. If their early access program is for real some actual information should start coming out this year... unless the fine print at the bottom of the early access application reads "please allow 3-5 years for processing"

Yeah. But even that marketing spiel years ago doesn't sound that good any more when HiSeq X spec is announced. Assuming they can come up with it in two years in the most optimistic scenario, Illumina will go to another gen. It seems more and more likely after waiting for so many years, they might still not be able to dethrone Illumina except for applications requiring long reads and minion for outdoor use.

I suppose their VC backers are wetting their pants now.:p

BBoy 01-17-2014 12:52 AM

Quote:

Originally Posted by ymc (Post 129904)
I suppose their VC backers are wetting their pants now.:p

Some of the VCs may not fully comprehend the full barriers to entry over and above the sequencing itself (sample prep, informatics pipelines, understood error profiles, etc) but they are no dummies. They had a new funding round very recently, so unless they completely misrepresented themselves to their investors there must be something there for real. I can't believe that anyone would give them any new money at this stage if they cannot produce some type of sequencing-related data. For example, PacBio did suck in $600M of VC money that will probably never be fully recouped, but they were not all smoke and mirrors and have mounted a niche comeback as of late.

ymc 01-17-2014 02:40 AM

Quote:

Originally Posted by BBoy (Post 129908)
Some of the VCs may not fully comprehend the full barriers to entry over and above the sequencing itself (sample prep, informatics pipelines, understood error profiles, etc) but they are no dummies. They had a new funding round very recently, so unless they completely misrepresented themselves to their investors there must be something there for real. I can't believe that anyone would give them any new money at this stage if they cannot produce some type of sequencing-related data. For example, PacBio did suck in $600M of VC money that will probably never be fully recouped, but they were not all smoke and mirrors and have mounted a niche comeback as of late.

I am sure the VCs saw nice thing when they put in money last round. However, they are likely to be caught in surprise for this mini-breakthough of HiSeq X that churns out 10x the throughput of HiSeq 2500. It seems now more and more likely nanopore can only be niche player that might only offer the VCs a break even return at best.:p

ZFHans 02-14-2014 06:51 AM

At least we can now start to judge for ourselves.
We got an invitation to join MAP and I suspect I'm not the only one.
I'm hoping we can soon produce some real data and make comparisons based on actual facts and not speculation.

NextGenSeq 02-14-2014 10:43 AM

We got an invitation too.

GenoMax 02-14-2014 01:06 PM

@NextGenSeq and @ZFHans: Does the "invitation" say when you are likely to actually get the kits?

ZFHans 02-15-2014 01:54 AM

The invitation is specific to the point of: "we look forward to working with you in the coming weeks."
More details will follow on the portal website that they have set up.

gringer 02-15-2014 05:03 AM

There's a fair bit of information on the Nanopore website now:

https://www.nanoporetech.com//techno...a-guide-to-map

Here's my rough summary:
  • Restricted open-access philosophy for results and software development via login at nanoporeonline.com
  • 6 week MAP cycles, 2 weeks for configuration, 4 for your own experiments. Burn-in cell in week 1, two experimental flow cells delivered week 3, two more week 5
  • Can duck out at any time with a deposit refund
  • Can continue on in the program for the next cycle, or stop and give someone else a go
  • Cost is $1,000 deposit (covers all MAP cycles) + $250 delivery (per cycle for multiple deliveries & returns) + taxes where relevant
  • ONP receives diagnostic statistics via the Grouper instrument software, but results are yours to keep
  • ONP requests that people remain tight-lipped until the end of the burn-in period, so people will be quiet about this for at least the next couple of weeks
  • Computer requirements are not mentioned on this page, although it is stated that Macs are not yet fully supported

Jeremy 02-17-2014 08:27 PM

Unfortunately my email was:

Thank you very much for taking the time to apply to join the MinION Access programme (MAP). We received a large number of applications from a broad range of applicants and unfortunately cannot invite every applicant at this time. Unfortunately we cannot offer you a place in the first wave of MAP however we intend to make more places available in the future and hope that you are happy to remain on our list of interested participants.
Once again we thank you for your interest. If you would prefer not to be considered for MAP in the future please email us on support@nanoporetech.com.

I hope those of us that did get in keep everyone posted in this thread.

ymc 03-21-2014 10:38 AM

I just noticed Oxford Nanopore thinks solid state nanopore is the future. They added Harvard's solid state nanopore team in 2011. If this new team develops fast enough, the current gen of protein nanopore might just be a stopgap product?

https://www.nanoporetech.com/technol...tate-nanopores


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