CPHx: Sponsored talk – Roland Wicki, Life Technologies

Ion Torrent Semiconductor Sequencing

Three sequencing technology concepts: Sanger, Post Light, Massively Parallel Sequencing.

PostLight fits somewhere in between sanger and massively parallel.  Long, fast, quantity.

Low cost convenient single use device..  Everything is on the chip.  55,000 euros for full machine, plus 17,000 euros for the server.

[They’ve trademarked “The Chip is the Machine”.]

Everything works on pH changes.  Very low cost, no cameras, not modified enzymes, etc.  It’s all nature.

Accuracy is 99.9% (from EdgeBio.)

Automatable, simple, quarterly updates and rapidly improving raw accuracy.

Chemistry.  Nucleotides are incorporated into DNA, releasing a proton.  That pH change can be measured.  If no nucleotide is incorporated, no pH change is detected.  If multiple bases are incorporated, a larger change is registerd.  [I assume this means they wash each of the bases over in sequence…  yep, it’s on the next slide.]

Raw accuracy is still improving all the time.  Homopolymer accuracy is now 99% for up to 6 bases being incorporated….  [nothing shown beyond that, however.]

Scalability: expect 100Mb in Q2 2011, 1Gb in Q4 2011.  [Some of that is longer reads.] [RE-EDIT:I have changed the above to reflect the accurate values.  The original numbers I had noted down were VERY wrong.  Please see my post here for more information]

Single day workflow available.  2 hour sequencing runs.

[Some discussion of products available… I don’t take notes on this type of stuff.  Consult your Life Tech rep if you want that info.]

Supported apps:

  • microbial
  • mitochondrial
  • amplicon
  • custom targetted
  • validation of whole genome/exome mutatinos
  • library assessment
  • RNA-Seq

Chip-Seq, Wholte transcriptome RNA-seq for human coming up with the next chip.  You need more coverage than you would get with the current chip.

Example given using DH10b data, available from Ion Torrent, BGI and EdgeBio.  You can get full data sets from Life Tech’s web page. [no url given.]

TargetSeq Enrichment Kits. announced recently.  Works for Exome Enrichment.

Details given for amplicon library prep.

You can use existing sanger-based amplicons on Ion Torrent.

You can also use PGM/Ion Torrent to do QC.  It’s a short run, so you can test library construction by sequencing small sets before tossing it on a higher throughput sequencer.

There is an Ion Community… if you want more info.

And a quick plug for BGI’s use of PGM to sequence E. coli found in recent outbreak.

 

9 thoughts on “CPHx: Sponsored talk – Roland Wicki, Life Technologies

    • I thought I heard it from the speaker twice. Once that it is coming out shortly, the other that it’s in Q4. I may have misheard, or misread the slide he was displaying at the time. I would suggest that the error is likely on my part, if you’ve been told otherwise.

  1. The speaker stated that the 316 chip would be out next month (originally stated as a Q2 release). The 318 chip is stated to be available broadly before the end of the year. It was also stated (by EdgeBio) that the current 314 chip gets 25MB/run rather than the original spec of 10MB/run.

  2. Whoever put “You can use existing sanger-based amplicons on Ion Torrent” on the slide doesn’t understand at all amplicon sequencing.

    There’s two major problems with this statement. The obvious one is that Sanger amplicons generally expect long read lengths, so it is already unlikely that what you are interested in will be covered by Ion, simply because they can’t cover much.

    But worse is the greater display of ignorance. Sanger sequencing does NOT perform well close to the primer. Hence, Sanger amplicons should always be designed with a good amount of space between the primer and what you care about. Indeed, I generally allow (unless the primer design is very constrained by genomic features) about 100 bp, though that is very conservative. As a result, a good Sanger design will not have the important regions read at all by Ion. You simply must design the amplicons to the technology!

    Of course, if they mean you can amplify and then fragment the amplicons, that’s a no brainer. Which is probably what they meant, if they understood the question at all, since Ion can’t handle long (>150nt) amplicons anyway; nobody in their right mind designs Sanger amplicons with 100 nt inserts (with 25×2 lost to targeting primers)!.

    • I have to admit, I was wondering about that too. I just figured I’d write it down, but consider me highly skeptical about that point.

  3. Pingback: CPHx: Ion Torrent 316 chip is due out in Q2, 2011 | Fejes.ca

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