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.]
- custom targetted
- validation of whole genome/exome mutatinos
- library assessment
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.