SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
Can you trust Pac Bio? math_guy Pacific Biosciences 23 11-19-2015 10:16 PM
Barcoding primers for Pac Bio Smriti Sample Prep / Library Generation 0 09-23-2015 01:44 PM
Is Nextera useful for Pac bio in future? Smriti Sample Prep / Library Generation 2 05-28-2015 10:14 PM
Pac Bio Developer Network just went up... ECO Pacific Biosciences 0 07-09-2010 07:43 AM
Pac Bio raises $100mill for sequencer commercialization ECO The Pipeline 0 07-15-2008 07:12 AM

Reply
 
Thread Tools
Old 03-18-2016, 12:59 PM   #21
spore
Member
 
Location: SF

Join Date: Nov 2015
Posts: 23
Default

Roche made an offer but Pacbio rejected it because it was too low. Honestly if they sold the company to Roche that would be the best thing to advance their technology. There's a lot of untapped potential they could reach by just throwing more money in R&D. Their cash situation has definitely held back the technology quite a bit.

As for the data, it's been about 5 months since launch and still no publicly released data. I think they'll be hitting a point soon where they wont really have any excuse on why data hasn't been released. It's either working or it isnt.

ONT is probably a worse company in terms of lying. It'll be years before they can reliably sell commercial products. Their miniIon has uses in academia but still needs a lot of work to put a dent in the commercial market. But they've lied so much over the past few years who knows what to believe.
spore is offline   Reply With Quote
Old 03-18-2016, 02:04 PM   #22
math_guy
Member
 
Location: san diego

Join Date: Apr 2013
Posts: 71
Default

That's the thing in bio, even up to the hardware "manufacturers": management tells lies and hopes that the engineers can make their lies true. I am not going to go out on a limb and say they're inflating their specs. I really want the specs to be accurate. If so, then the long term with Pacific Bio looks good. I'll be a customer that they dislike, but I'll use their machines and consumables. And I'll use them a lot.

Someone should buy Oxford AND Pacific Bio. That way they can compete with Illumina in nano-pore. Oxford, if they end up working, would be perfect for every lab and they would be perfect for hospitals and some clinics. The Sequel is perfect for medium and larger labs, sequencing service providers, large clinical trials, research hospitals, and the most important of all: government cancer-research money.
math_guy is offline   Reply With Quote
Old 03-20-2016, 12:34 PM   #23
Ola
Member
 
Location: Sweden

Join Date: Aug 2011
Posts: 30
Default

Quote:
Originally Posted by math_guy View Post

Lastly, I hope Oxford beats everyone to it and I can buy their solution instead. I rarely see posts here in the Oxford sub. In my opinion, it should be more active.
I guess it is because they have their own community so you are more likely to get a response there. If you have not already, now would be a good time to try out the MinION. I am sure you could spare $1000 if you are thinking of buying three Sequels, without seeing any data... I find it strange that even their Sequel brochures only show RS-II results, looks like they had to rush it. Specs loks good and of course CCS accuracy is nice but I don't see how it could scale to be competitive with 10x on X10 and the next gen nanopores.
Ola is offline   Reply With Quote
Old 03-21-2016, 08:09 AM   #24
math_guy
Member
 
Location: san diego

Join Date: Apr 2013
Posts: 71
Default

Quote:
Originally Posted by Ola View Post
I guess it is because they have their own community so you are more likely to get a response there. If you have not already, now would be a good time to try out the MinION. I am sure you could spare $1000 if you are thinking of buying three Sequels, without seeing any data... I find it strange that even their Sequel brochures only show RS-II results, looks like they had to rush it. Specs loks good and of course CCS accuracy is nice but I don't see how it could scale to be competitive with 10x on X10 and the next gen nanopores.
We will begin an attempt to review Oxford and the MinION. I am starting to get even more uncertain of Pacific Bio. I am still wondering why we have seen very little data on the Sequel. It makes me feel that there is something going on. But maybe I am just being too critical. However...how long does it take to start distributing some data? Shouldn't Pacific Bio be releasing some as well, by this point in time?

What makes you feel that the system couldn't scale very well compared to unannounced technology? Is there a known cap with Pacific Bio's tech?
math_guy is offline   Reply With Quote
Old 03-21-2016, 09:44 AM   #25
spore
Member
 
Location: SF

Join Date: Nov 2015
Posts: 23
Default

Quote:
Originally Posted by Ola View Post
I guess it is because they have their own community so you are more likely to get a response there. If you have not already, now would be a good time to try out the MinION. I am sure you could spare $1000 if you are thinking of buying three Sequels, without seeing any data... I find it strange that even their Sequel brochures only show RS-II results, looks like they had to rush it. Specs loks good and of course CCS accuracy is nice but I don't see how it could scale to be competitive with 10x on X10 and the next gen nanopores.
Actually the Pacbio Sequel technology scales the best out of all the technologies. They integrated all the optics onto a camera sensor so it's not hard at all for them to just use a higher res sensor to increase the thoughput. They already expect in 2017/2018 time frame to have a chip with 5 million ZMW's and they can keep increasing that number easily because the sensor technology is already there. The 5 million ZMW sensor would already give cheaper sequencing than the X10. Not to mention they usually 2x their read length every year too.

Illumina was caught off guard and quickly announced firefly for late 2017. This is essentially doing the same thing as pacbio did with Sequel. But it won't scale as well because illumina has to use larger wells that take up more space so you can't fit as many sequencing wells on a chip as pacbio can. Illumina is also read length and flow limited. They need to totally new technology to keep up with Pacbio in the long run.

Nanopore scales by just throwing more flow cells in the same instrument. This isn't really a good way to scale. It's VERY difficult to make nanopore reliably. That's why we don't see them coming out with new chips with 100k+ nanopores on them. Until they can show they have found a scalable way to increase the nanopore count then the tech is not that scalable. Which probably won't happen until semiconductor nanopores are able to be fabricated.

Right now Pacbio definitely has the most scalable technology.
spore is offline   Reply With Quote
Old 03-21-2016, 10:47 AM   #26
Ola
Member
 
Location: Sweden

Join Date: Aug 2011
Posts: 30
Default

Quote:
Originally Posted by spore View Post
Actually the Pacbio Sequel technology scales the best out of all the technologies. They integrated all the optics onto a camera sensor so it's not hard at all for them to just use a higher res sensor to increase the thoughput. They already expect in 2017/2018 time frame to have a chip with 5 million ZMW's and they can keep increasing that number easily because the sensor technology is already there. The 5 million ZMW sensor would already give cheaper sequencing than the X10. Not to mention they usually 2x their read length every year too.

...

Nanopore scales by just throwing more flow cells in the same instrument. This isn't really a good way to scale. It's VERY difficult to make nanopore reliably. That's why we don't see them coming out with new chips with 100k+ nanopores on them. Until they can show they have found a scalable way to increase the nanopore count then the tech is not that scalable. Which probably won't happen until semiconductor nanopores are able to be fabricated.

Right now Pacbio definitely has the most scalable technology.
That is good to know, I was not aware of the differences in optics between the two systems. It is great if it really is as scalable as you say.

It may well be difficult to make reliable nanopores, but the real challenge would be to get data out from 100k+ pores simultaneously (look at Proton PII and PIII). With scalable I thought more about producing instruments and sequences, not the actual detection units per flowcell. Running faster with more reads coming off each pore is obviously also one way to scale.
Ola is offline   Reply With Quote
Old 03-21-2016, 02:42 PM   #27
AllSeq
Registered Vendor
 
Location: San Diego, CA

Join Date: Oct 2013
Posts: 138
Default

Quote:
Originally Posted by spore View Post
Actually the Pacbio Sequel technology scales the best out of all the technologies.
From our perspective, PacBio's advantages are true long reads and low consensus error rates. Total output improvements (in terms of Gb and # of reads) hasn't really been their strength (although the Sequel does look like a significant step up).

PacBio has done a decent job of scaling over the past couple of years, but they haven't scaled nearly as fast as Illumina (in terms of output per run or output per unit time). Has something changed that makes you think they'll start scaling faster than the ~4x/yr improvements (from a relatively small base) that they've achieved over the past few years?
__________________
AllSeq - The Sequencing Marketplace
info@AllSeq.com
www.AllSeq.com
AllSeq is offline   Reply With Quote
Old 03-21-2016, 02:44 PM   #28
spore
Member
 
Location: SF

Join Date: Nov 2015
Posts: 23
Default

Yeah the optics between the two systems was the big change. That's why the instrument is now 1/4 of the size.

Of course all of this depends on Pacbio actually proving Sequel works. It's been 4 months and still no hard data. I would assume they should have ran plenty of internal experiments and published the data by now. My guess is they won't publish anything that has worse data than the RS gives. If they havent published anything by may then I think management jumped the gun and launched a product that wasn't ready.
spore is offline   Reply With Quote
Old 03-21-2016, 02:58 PM   #29
spore
Member
 
Location: SF

Join Date: Nov 2015
Posts: 23
Default

Quote:
Originally Posted by AllSeq View Post
From our perspective, PacBio's advantages are true long reads and low consensus error rates. Total output improvements (in terms of Gb and # of reads) hasn't really been their strength (although the Sequel does look like a significant step up).

PacBio has done a decent job of scaling over the past couple of years, but they haven't scaled nearly as fast as Illumina (in terms of output per run or output per unit time). Has something changed that makes you think they'll start scaling faster than the ~4x/yr improvements (from a relatively small base) that they've achieved over the past few years?
Previous throughput increases on the RS were because of RL increasing. With Sequel they have two area's they can increase throughput with
1) RL
2) # of ZMW's

I assume they should be able to do better than the 4x/year because they can now come out with chips with a lot more ZMW's. I saw some slides from a conference where Pacbio expects a 5-6million ZMW chip by 2018. So that's a 6x increase just on ZMW's. If you assume they keep doubling their readlength every year that would add another 4x over the next two years. So that would be about a 24x increase over 2 years (assuming a 6M ZMW chip and ~50k readlength by 2018).

They can also tweak the speed of the sequencing reaction to increase the throughput. This is something they havent done yet though.

If this technology does work then they will catch up to Illumina fairly quickly. That's why I think the best option is for them to sell to Roche. Roche can dump millions into the company and really let the technology thrive.
spore is offline   Reply With Quote
Old 03-22-2016, 05:19 AM   #30
Ola
Member
 
Location: Sweden

Join Date: Aug 2011
Posts: 30
Default

Quote:
Originally Posted by math_guy View Post
We will begin an attempt to review Oxford and the MinION. I am starting to get even more uncertain of Pacific Bio. I am still wondering why we have seen very little data on the Sequel. It makes me feel that there is something going on. But maybe I am just being too critical. However...how long does it take to start distributing some data? Shouldn't Pacific Bio be releasing some as well, by this point in time?

What makes you feel that the system couldn't scale very well compared to unannounced technology? Is there a known cap with Pacific Bio's tech?
One limitation with the PacBio is that it relies on very long reads since it (currently) only does one read per ZMW, and increased read lengths does not increase throughput if you can't make libraries to match. And "throwing in more flowcells" is not a bad thing if they are cheap. Will see soon how the new chemistry and base callers perform on MinION, I am hoping PacBio can keep up but with no Sequel data out yet I would not bet on it.

For those who have not followed the recent ONT updates you can watch it here: https://www.youtube.com/watch?v=nizGyutn6v4

Last edited by Ola; 03-22-2016 at 05:21 AM.
Ola is offline   Reply With Quote
Old 03-22-2016, 10:45 AM   #31
spore
Member
 
Location: SF

Join Date: Nov 2015
Posts: 23
Default

I'm not sure if the flowcells are exactly cheap. And I'm sure it's going to be hard to manufacture those nanopores in high volume. This isn't a semiconductor process. ONT is really cool but they definitely have a bit of work to do before it's a large scale commercial ready product.

The no Sequel data is concerning. I fully expected to see at least some data come out from Pacbio by now. I understand there's bugs and and stuff to work out but if you can't even get 1 good data set to show off in 4 months then I'm thinking there may be bigger issues we don't know about.
spore is offline   Reply With Quote
Old 03-23-2016, 08:13 AM   #32
math_guy
Member
 
Location: san diego

Join Date: Apr 2013
Posts: 71
Default

Quote:
Originally Posted by spore View Post
I'm not sure if the flowcells are exactly cheap. And I'm sure it's going to be hard to manufacture those nanopores in high volume. This isn't a semiconductor process. ONT is really cool but they definitely have a bit of work to do before it's a large scale commercial ready product.

The no Sequel data is concerning. I fully expected to see at least some data come out from Pacbio by now. I understand there's bugs and and stuff to work out but if you can't even get 1 good data set to show off in 4 months then I'm thinking there may be bigger issues we don't know about.
The lack of data concerns me too. I wonder if ANYONE has seen anything yet?
math_guy is offline   Reply With Quote
Old 03-23-2016, 09:05 AM   #33
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,966
Default

Dr. Keith Robinson has a roundup of news about Sequel.

Last edited by GenoMax; 03-23-2016 at 11:20 AM. Reason: Incorrect
GenoMax is offline   Reply With Quote
Old 03-23-2016, 10:34 AM   #34
Ola
Member
 
Location: Sweden

Join Date: Aug 2011
Posts: 30
Default

Quote:
Originally Posted by GenoMax View Post
Dr. Keith Robinson has a roundup of news about Sequel.
No, that is an old post describing the introduction of the RS system. Things have changed a lot: "Read lengths decay exponentially -- but with lots around 1Kb and quite a few around 5K", "The instrument is clearly a ways from really threatening Illumina & SOLiD".

Maybe he has a new (blank) page with Sequel news...

I know nothing about the manufacturing cost of nanopore flowcells, but given that the current version is $500 i would think it is substantially lower if it is detached from the ASIC.
Ola is offline   Reply With Quote
Old 03-23-2016, 11:21 AM   #35
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,966
Default

It showed up with a new tag/date in my inbox.

But you are right . It appears that Dr. Robinson just removed an image and blogspot.com tagged the entire post as new. So we still remain in dark about Sequel data/performance.
GenoMax is offline   Reply With Quote
Old 03-23-2016, 05:13 PM   #36
AllSeq
Registered Vendor
 
Location: San Diego, CA

Join Date: Oct 2013
Posts: 138
Default

Quote:
Originally Posted by GenoMax View Post
It appears that Dr. Robinson just removed an image and blogspot.com tagged the entire post as new.
Keith wasn't trying to pull a fast one on you. He got a DMCA takedown notice for an image of the RSII (Why? No idea.) Rather than fight it, he just removed the image. Apparently he wasn't able to prevent it as showing up as a new post.
__________________
AllSeq - The Sequencing Marketplace
info@AllSeq.com
www.AllSeq.com
AllSeq is offline   Reply With Quote
Old 04-14-2016, 03:51 PM   #37
AllSeq
Registered Vendor
 
Location: San Diego, CA

Join Date: Oct 2013
Posts: 138
Default

Quote:
Originally Posted by math_guy View Post
The lack of data concerns me too. I wonder if ANYONE has seen anything yet?
We still haven't seen any of the data ourselves, but William Blair (an equity research firm) has had some positive feedback from users. From their research report earlier today:

"Early feedback from users of PacBioís Sequel has been positive. Initial user experience suggests that the Sequel is performing essentially in line with the RSII from a read length and quality perspective. Early users have been able to achieve throughput specs close to advertised levels (which is unusual for a platform in early access). Initial users of the Sequel are likely sophisticated RSII users, and thus it is unclear how this experience will translate to general commercial users, but we are encouraged by Sequel launch commentary thus far."
__________________
AllSeq - The Sequencing Marketplace
info@AllSeq.com
www.AllSeq.com
AllSeq is offline   Reply With Quote
Old 04-14-2016, 04:14 PM   #38
spore
Member
 
Location: SF

Join Date: Nov 2015
Posts: 23
Default

Thanks for sharing that information. How does one get access to their research reports?
spore is offline   Reply With Quote
Old 04-14-2016, 07:04 PM   #39
AllSeq
Registered Vendor
 
Location: San Diego, CA

Join Date: Oct 2013
Posts: 138
Default

I'm not quite sure. We're on their distribution list because we periodically consult for them on the genomics market.
__________________
AllSeq - The Sequencing Marketplace
info@AllSeq.com
www.AllSeq.com
AllSeq is offline   Reply With Quote
Old 07-21-2016, 07:12 PM   #40
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,223
Default

Quote:
Originally Posted by math_guy View Post
Yes. We prefer it in our labs. Labs steal every idea they can get their hands on in our experience. I come from a different field. Bio is the worst. Too much money and not enough smart people. Makes people just want to steal instead of coming up with it on their own. I know.... I know... That will make people mad here. But I have never seen so much theft of ideas in my life until I entered the world of biotech.

So...yeah...without trying to come off as being rude: we only trust ourselves. Why? Cuz we have had some of our work stolen before. In fact, by people at UCSD. In fact, if we had not hidden and made fake data, we would never have caught them. The best part of their theft is that they still hit us up for more money after getting caught. Bio...you have to love it!

Also, I am guessing this part of my post will irritate many people here. I miss my old field...and I know...someone will tell me to get the heck outta their field and please leave them alone. I beat you to that response
I wonder if you are still interested to buy Sequel even though there is no data out yet. I do not have one for sale.
nucacidhunter is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:04 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO