Ion Torrent versus 454 FLX Junior

[rubenken]

Any thoughts on whether either system is favorable for diagnostic applications and which might be favored?

[krobison]

Junior has the jump to get in. Cost of ~$2K/run (corrections welcome) in reagents means it will probably still be necessary to multiplex samples for many applications. Longer read length will be valuable -- when needed.

Ion Torrent isn't here yet. I think the upfront cost is about 1/2 ($100K vs. $200K), though I've seen different claims for Junior. Sample prep gear for both may be similar, which would narrow the relative (but not absolute) cost differential. Ion Torrent will be similar number of reads but shorter reads at 1/4 the run cost (right?) -- if it comes in as advertised.

I'd give Ion Torrent the edge. If the chemistry can be pushed to 454-like read lengths without upping the cost (likely, given that most of the chemistry cost is in the chip), then 454 is is big trouble.

See also my blog posts Worse Could Be Better and http://omicsomics.blogspot.com/2010/08/Who Has The Lead in 1K Genome Race?

[henry.wood]

I don't know exactly what you are planning, but some colleagues of mine have been using an illumina for diagnostic sequencing. They do multiplexed sequencing of long PCR products. If you want to know more, have a look at http://www.ncbi.nlm.nih.gov/pubmed/20127978

[SrScientist]

Life Tech mentions that Ion Torrent instrument and run will be even cheaper than Junior. And if I have a look into the actual "specs", I see no reason to purchase a Junior.

[Jacky76]

What's better? depends on what you will do

I'm not sure what you are planning, there are many kinds of diagnostic sequencing and most of them need longer read length in my experience. I guess many applications are replacing Sanger, and most of amplicons have loger than 300bp something. If you want to look into the mutations like insertion, deletion, you will have problem with the short read length. Furthermore, longer reads means better ability for haplotyping. Many of diagnostic sequencings need to see haplotypes. But if you think 100bp is enough for your application, you will take advantage with IT. But the concern here is their performance was not yet validated than GS Junior. And it is the biggest challenge at improving sequencing technology that lengthening the read length. So I don't think Ion Torrent can have enough reads soon. GS Junior has been being tested so far for diagnostic purpose by MDs, and has been getting good evaluation. But there is still concern on it's result. GS Junior still has difficulty on reading homopolymeric regions.

[dc3000]

Any updates here, especially for using the Ion Torrent for amplicon sequencing (16S, etc.)?

[colindaven]

Try this, if you haven't already:

Article (Loman2012) Loman, N. J.; Misra, R. V.; Dallman, T. J.; Constantinidou, C.; Gharbia, S. E.; Wain, J. & Pallen, M. J. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol, Centre for Systems Biology, University of Birmingham, Birmingham, UK., 2012