Tag Archives: IonTorrent PGM

More Updates: Illumina & IonTorrent

Quarter 4 of 2014 seems to be another exciting one for Next Generation Sequencing. Beside the chemistry update for PacBio RSII also Illumina and IonTorrent / ThermoFisher announced two major improvements / achievements:

  • Chemistry update for the Illumina HiSeq X Ten and the HiSeq 2500 Rapid Run
    The new v2 reagent kit for the HiSeq X Ten supports a PCR-free sample preparation kit, which eliminates amplification during the library preparation. So far only sample preparation kits with PCR were possible, which sometimes results in a lower quality of challeging genomic regions.
    The new v2 reagent kit for the HiSeq 2500 enables users to sequence 2x 250 bp and the new chemistry therefore delivers up to 300 Gbp of data in only 60 hours. (Press Release)
    To my opinion Illumina proves once more that NGS is highly dynamic and that their continous update for existing systems is the key for their success (the latest financial report confirms that Q3 of 2014 with a growth of 10% is the strongest since 2011 for Illumina (Fierce Medical Devices)).
  • IonTorrent goes diagnostic
    The Ion PGM Dx System is now also CE-Marked for in vitro diagnostic (IVD) use in Europe. Thermo Fisher Scientific believes that the CE-mark “will enable European clinical laboratories to more easily […] implement new […] diagnostic assays” (Press Release).
    In September they announced already that the PGM is now listed with the U.S. FDA as a Class II Medical Device.
    To my opinion the clearance for diagnostic use in Europe as well as in the U.S. will further strengthen the position of the Ion PGM in clinical laboratories.

IonTorrent Upgrade

Just some days ago we discussed the dynamics in NGS and here we are with some news. Life Technologies Corporation announced that the new software v3.0 for the IonTorrent PGM consistently delivers 99.9% consensus accuracy for both short and long homopolymer regions and increases the frequency of correctly called insertions, deletions and homopolymer sequences by two-fold (Press Release LIFE).

In addition to the read accuracy also the read length increased with the launch of the new kit to 400 bp. The aim of the company is to improve their system further for microbial applications (PR LIFE).

But not only improvements in bacterial identification is on the priority list for LIFE’s RnD team but also more innovations in the area of diagnostics. A new AmpliSeq(TM) sample ID panel will increase the confidence during data analysis and a new kit is soon to be launched (PR LIFE).

I think from a customer’s perspective it is a good idea to further improve the technology in several areas since there could be some cross-linking innovations. But it also bears the risk that some competitors, focussing on a specific application, will adapt their system more quickly. But of course these are only speculations. So what is your opinion?

 

Comparison of NGS technologies – just a waste of time?

As already mentioned in our latest blog post Michael Quail and his team from the Sanger Institute published a comparison of the Ion Torrent PGM, the PacBio RS system and the Illumina MiSeq (BMC Genomics). This study and all the others performed recently couldn’t determine one clear winner as each system has its own advantages.

But really interesting are now the statements of the spokespersons from the different companies in a recent article from Julia Karow in GenomeWeb. They all agree on the same thing: the data collected in the publication have been true in 2011, but are outdated by now since a lot of effort is put into innovation. Every instrument performs a lot better now. So what is our conclusion? That comparisons for NGS technologies are just a waste of time? For the Sanger institute it means that they invested in 3 new MiSeq’s since the Illumina pipeline is already available. For me, these comparisons are also valuable for all other institutes. Although maybe outdated, they highlight the strength and weaknesses of each technology and help to decide where to invest thousands of dollars. What do you think?