Tuesday, 20 August 2013

Ready for Avalanche?

It's been a while (I remember rumors more than 1 year ago) since Life Tech started talking about a new chemistry based on isothermal amplification that promise to eliminate emPCR, shorten clonal amplification down to less than 1h and provide better uniformity...They called it Avalanche...But no more has been revealed in the past months, such that Avalanche was becoming like a mythological creature: sure it's fascinating, but does it really exist?

However keep your new stuff secret since the time of commercial release seems to be a common way of acting in the competitive field of NGS technology...and now finally Avalanche is ready to hit our bench and provide the long waited improvement for SOLiD and Torrent sequencing platforms.
Indeed, researchers from Life Technologies has recently published on PNAS a paper demonstrating the feasibility, efficiency and rapidity of the new method. As anticipated, it's based on isothermal amplification of a properly prepared DNA template using the bst DNA polymerase and substrate immobilized primers. Citing the abstract, it use "a template walking mechanism using a pair of low-melting temperature (Tm) solid- surface homopolymer primers and a low-Tm solution phase primer". Authors report results obtained with the new method applied on a SOLiD 5500 W flowchip and they are quite exciting: reaction time of slightly more than 30 min with high percentage of monoclonal colonies and 3- to 4-fold more mapped reads than with traditional method and easy paired-end protocol.

Since the procedure reported in the paper is developed on SOLiD technology, I expect that the new chemistry will be commercially available in short time on this platform...However, I'm wondering if Life Technology is already working to extend this innovation also to Torrent sequencers and if they will introduce Avalanche with the PII chip (announced to be out in these months) or with the PIII ( probably in the first half of 2014). The method demonstrated in the paper require surface immobilized primers on a flowcell, so they have to adapt it to work on the small beads that are required for the PGM and Proton chips...or they have to re-think the chips themselves to avoid use of beads, but I think this solution is not so easy to apply on the current sequencer machine. Another question that bother most of the Torrent cutomers: will Avalanche be compatible with the current library/template preparation equipment or we will have to buy some new expensive piece to actually do the upgrade?

Now waiting to be trampled by the Avalanche!

For more technical details read the full paper:
Isothermal amplification method for next-generation sequencing. 
Ma Z, Lee RW, Li B, Kenney P, Wang Y, Erikson J, Goyal S, Lao K. 

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