AGBT Talk: Life Tech – Ion Torrent

Title: Scaling Semiconductor Sequencing.

  • Sequencing on a semi conductor chip.  Uses known technology for chips, but changes way we do sequencing.  Chip is actually the machine.
  • Should allow scaleup every 6 months.
  • Chemistry is “post-light” sequencing.  Chemistry requires no optics, so no quenching.  Coverage is very uniform.
  • Native polymerases and native nucleotides – which also makes it low cost.
  • Chips start @ $250
  • Speed is also a benefit.  2 hour seq. runs.
  • Sample prep is decoupled from sample prep, which can be done in batch.   Many improvements coming in sample prep – currently takes about 8 hours, should be about 2 hours by the time optimizations are done.
  • Rapid performance improvements [nice graphic, but can’t copy it down for you… I’m sure they’d share it, however.]

Chad Nusbaum from Broad Institute will give the main talk:

Title: Implementation and applications…. something like that.  [ (-:  ]

  • Key tech:
    • Does it do something we need
    • can it do it better
    • can it provide special benefit?
    • Is there enough need to make it worth the investment.
  • What’s appealing about ion torrent:
    • fast, simple, cheap
  • “[Speed] matters more now than it did then.”
  • Requires little infrastructure.
  • “lightweight process”
  • Easier to trouble shoot
  • machine is small and inexpensive
  • supply chain is simple too.
  • “Tactical”
    • Speed – quick turn around on processes.
    • simplicity means esier optimization, etc
  • Applications:
    • Usual stuff
    • Viral sequencing,
    • QC large sequencing pools
    • QC of targetted capture samples
    • Exon capture experiments
    • Transcriptomics/cDNA
    • Genome assembly.
  • Did a tumour sequencing validation expt.
    • After filtering, you get 10-100 variations per tumour.
    • showing validation results. 72/93 variants were called correctly (from the “hardest” set.  [not sure why they were hard… microphone keeps cutting out, and may have missed something.]
    • more than 99% of reads yield assignable barcodes (for a pooled library).
  • Lab optimization: (slide on optimization cycle….  not particularly informative.)
  • current chip have 7m wells.
  • Observed low GC bias.
  • good representation of homopolymers
  • some computational approaches being worked on… wont talk about it.

Summary: fast, signifiant performances, demonstrated utility.

[Neat talk, and very quick.. now off to the meetup!]

4 thoughts on “AGBT Talk: Life Tech – Ion Torrent

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  2. He claimed that the PGM was going to be useful for transcriptomics? It doesn’t seem like it has remotely enough reads for this to be a good application. The last I heard was that the 316 chip with 7M sensors would produce up to 400k reads. If you assume you need only 10M reads per sample, that would take 25 runs over 2 full days at a cost of at least $6250, assuming $250/chip; $12,500 at $500/chip, which is what I think the 316 will cost).

    • I’m not sure about your math (as I haven’t worked it out for myself), but there are transcriptome experiments for which you don’t need a lot of depth – particularly for microbiome experiments where Illumina’s depth would be overkill. I’m pretty sure this is not in reference to doing cancer transcriptomics or similar experiments.

      • Anthony,

        My estimate of 10M reads is the minimum needed for human expression profiling (with up to 100M needed for a more comprehensive view of the transcriptome), so the PGM is currently not suitable for these experiments. However, as you’ve pointed out, it may be just fine for simple prokaryotic transcriptomes (and a full HiSeq or SOLiD run would indeed be overkill). I’m just not sure how big of a market that is.

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