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Old 06-26-2013, 05:33 AM   #61
NextGenSeq
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Avalanche is more than a rumor. LifeTech has shown actual data of on-chip amplification in their presentations.
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Old 06-26-2013, 05:35 AM   #62
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is that presentation online?
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Old 06-26-2013, 07:04 AM   #63
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I was talking to a LifeTech guy (a technical specialist, not R&D, so take it for what it's worth) the other day and he mentioned Avalanche. As I'm still not clear on what it is exactly I asked him for more detail. While he didn't explain how it works, he did tell me that it will be used on the PIII chip and that he has seen perfect 600 bp reads obtained in house with it. If that's true, and if we actually see it at the customer level, that will really be something.

*Of course, this is all heresay at this point, so take it for what it's worth, which might not be much. We've heard similar grand claims from ONT and have yet to actually see anything available to us. It's nice to dream.
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Old 06-26-2013, 07:06 AM   #64
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it sounds great...and dreaming is fun (just thinking of water skiing with my own yacht) but I prefer things that are usable right now.
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Old 06-26-2013, 10:22 AM   #65
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Quote:
Originally Posted by ajthomas View Post
I was talking to a LifeTech guy (a technical specialist, not R&D, so take it for what it's worth) the other day and he mentioned Avalanche. As I'm still not clear on what it is exactly I asked him for more detail. While he didn't explain how it works, he did tell me that it will be used on the PIII chip and that he has seen perfect 600 bp reads obtained in house with it.
Ion has this perverse obsession with "the perfect read" -- which is utterly useless from a practical standpoint. There may be one perfect read, but you can't tell which one it is in actual use. It's a meaningless statistic that is almost certainly distracting them from focusing on the real issues. It makes about as much sense in this situation as one perfect limousine.
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Old 06-26-2013, 01:03 PM   #66
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News today is that Jonathan Rothberg is leaving Life Tech. Hopefully it is just the outcome of putting an entrepreneurial guy in a huge merged company rather than any concerns about the future of the Proton system.

http://www.forbes.com/sites/matthewh...-technologies/
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Old 06-26-2013, 07:23 PM   #67
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Quote:
Originally Posted by ajthomas View Post
I was talking to a LifeTech guy (a technical specialist, not R&D, so take it for what it's worth) the other day and he mentioned Avalanche. As I'm still not clear on what it is exactly I asked him for more detail. While he didn't explain how it works, he did tell me that it will be used on the PIII chip and that he has seen perfect 600 bp reads obtained in house with it. If that's true, and if we actually see it at the customer level, that will really be something.

*Of course, this is all heresay at this point, so take it for what it's worth, which might not be much. We've heard similar grand claims from ONT and have yet to actually see anything available to us. It's nice to dream.
600 bp reads? on a PIII chip? Sounds highly suspect to me. They are still trying to get 400 bp reads on a PII chip from the field application specialist I spoke to last month when we were getting training on our new proton. From what I heard the PIII chip is still quite a while away, since the PII chip isn't even release yet it makes business sense to focus all R&D on that. Even the PI chip only has 100 bp reads because quality degrades when the reads go longer.

Since the smaller chips can get longer reads and the large chips can't I can only assume that there is some sort of noise interference introduced by scaling the chip up.
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Old 06-27-2013, 12:42 AM   #68
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Do you have a Proton in your lab in Thailand? How is it performing?
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Old 06-27-2013, 12:46 AM   #69
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We do, so far has only run the test human samples. So nothing really to report. But they worked fine. We will do an RNA-seq run soon.
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Old 06-27-2013, 12:53 AM   #70
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Would be great to see some stats once you have some runs on. Thanks ...
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Old 06-27-2013, 03:30 AM   #71
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There are some statistics from the throughput competition. Maybe some of the users could share more info.

http://resource.lifetechnologies.com...2013/WE211164/
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Old 06-27-2013, 08:28 AM   #72
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Quote:
Originally Posted by Jeremy View Post
600 bp reads? on a PIII chip? Sounds highly suspect to me. They are still trying to get 400 bp reads on a PII chip from the field application specialist I spoke to last month when we were getting training on our new proton. From what I heard the PIII chip is still quite a while away, since the PII chip isn't even release yet it makes business sense to focus all R&D on that. Even the PI chip only has 100 bp reads because quality degrades when the reads go longer.

Since the smaller chips can get longer reads and the large chips can't I can only assume that there is some sort of noise interference introduced by scaling the chip up.
That is what he said, but as I said, he was a technical specialist, not an R&D guy, so it's 2nd hand at best. It's not hard to imagine details getting lost along the way. He did say, however, that it was with Avalanche, so it is a completely different amplification procedure and may not be comparable to what we're doing now with beads. Based on what he said, I was left with the impression that the PIII chip will work with Avalanche and not with beads at all.
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Old 06-27-2013, 05:42 PM   #73
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Well I hope he is right, 600 bp reads on such a high output chip would be great.
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Old 08-26-2013, 04:01 PM   #74
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Default Custom amplicons

Hi,

We´re currently thinking about buying the PGM, and this thread has been very helpful (We already have the MiSeq).

One of our principle drivers for buying the PGM is for the custom amplicon technology; we want to sequence small panels of genes in large numbers of patients.

When designing the panel on the Illumina Design Studio, many of the targets gave 0% design efficiency on the first attempt. We contacted Illumina, and they basically said ´yeah, we know, it doesn´t work so well´. This is in contrast to their custom exome, which works very well.

On the other hand, the Life/Ion version of this seems to work very well on the design level.

Does anyone have experience with either the Ion or Illumina custom amplicon methods? Any thoughts or tips? I´m thinking that with our throughput it´s worth buying the PGM for this method alone, but I´m worried about the negative comments I´ve seen about PGM.

Thanks!
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Old 08-27-2013, 10:31 AM   #75
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If you can get an amplicon panel to amplify targets properly, why not still use the MiSeq for readout?
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Old 08-30-2013, 04:55 PM   #76
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What are the important drivers for your decision?
Total throughput? Turn around time? Analysis?
PGM run is hours, but Miseq can produce more total data in 1-3 days.
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Old 09-03-2013, 04:45 AM   #77
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Re: jrbell71: as far as I know, the Life panels are not compatible with running on MiSeq (some people are trying to work out protocols I believe). Also, since the gene panels are small (about 13 kb cumulative sequence), the MiSeq would be overkill as it gives way more sequence than necessary.

Re: snetmcom: The main driver is good quality sequence for mutation detection. We don´t need a very rapid turnaround. A good depth of coverage, and relatively straightforward analysis would be nice!

Thanks.
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Old 09-25-2013, 04:36 AM   #78
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so what are they ever going to release the PII chips or what?
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Old 09-25-2013, 06:46 AM   #79
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Quote:
Originally Posted by repogue View Post
Re: jrbell71: as far as I know, the Life panels are not compatible with running on MiSeq (some people are trying to work out protocols I believe). Also, since the gene panels are small (about 13 kb cumulative sequence), the MiSeq would be overkill as it gives way more sequence than necessary.

Re: snetmcom: The main driver is good quality sequence for mutation detection. We don´t need a very rapid turnaround. A good depth of coverage, and relatively straightforward analysis would be nice!

Thanks.
Agree on the quality of the Illumina data. It is quite accurate. Illumina has the homopolymer run, and in my experience a higher frequency of insertion and deletions.

And yes, people are working on cross-platform panels that our interoperable. We currently have a few panels in beta testing that work on both Illumina and Ion Torrent with good results. The short of it, it is possible to do with careful attention to platform differences and sequence error profiles. Each assay needs careful characterization of its systematic differences in performance between the platforms. We have one methodology publication in pre-press production which should be out next month describing the general approach, and an expanded article on the method for interplatform interoperability with amplicon panels in the upcoming year.

-Tom
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Old 09-27-2013, 04:56 AM   #80
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Agree on the quality of the Illumina data. It is quite accurate. Illumina has the homopolymer run, and in my experience a higher frequency of insertion and deletions.
Huh??? That's backwards from my experience; did you mean "Ion" where you wrote "Illumina"?
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