Supposedly, if you need long reads of high quality and throughput, you should be using GS FLX+, yielding 750-800 peak read length, from Roche/454, right? Illumina reads are getting longer, but 250 is for now the limit (notwithstanding the 300 bp run done by the broad). IonTorrent promises 400 bases, but we will have to see what the quality is going to be. And PacBio, well we all know they are long, but with relatively low throughut and quality peaking at 85% – 86% accuracy (useful nonetheless).
Commercially, GS FX+ had been around for more than half a year. So far, the community is reporting some success, see this thread at SeqAnswers. But, there are problems all around when you talk to people. Our own centre (the Norwegian Sequencing Centre) got the upgrade in August. I’ll spare you the details on numerous control/test fragment runs, short read runs etc, but the bottom line is that we still haven’t been able to sucessfully sequence a FLX+ library on our GS FLX+. Right now, we are having a service visit, and I intend to chain the guy to the instrument until we see some real good data from one of our own libraries…
There is another thing that surprises me too: I am attending PAGXX, the Plant and Animal Genome conference in San Diego, where Roche is one of the main sponsors. However, when you look at the little text they have as an exhibitor, well, let me just quote a part of it for you (source):
“Roche Applied Science introduces the latest innovations in reagents and instruments for genomics research with the launch of our new Titanium reagents generating 400 to 500 bp sequencing read lengths using 454’s ultra-fast pyrosequencing technology for whole genome sequencing projects.”
What? ‘latest innovation’, ‘our new Titanium reagents’, ‘400 to 500bp’? Nothing about GS FLX+, 700-800 bp, let alone 1000 bp reads? Surely, this is a marketing glitch, right, just somebody who forgot to update the standard text. Well, today I passed the booth Roche has here at PAGXX. Sure, there was the obvious GS FLX instrument. But, to my amazement, it was a GS FLX, NOT a GS FLX+! You can tell since the loading bay for reagents is bigger on the GS FLX+, and it says ‘GS FLX+’ on it as well. The exhibited instrument had none of that.
Should we read anything into this? Is there no pride in the Roche system about their uniquely long reads? Surely there is, they have talks around the longer reads, for example here and here, and a workshop with GS FLX+ in the title: “De Novo Assembly of Complex Genomes: The GS FLX+ System Makes a Difference.”
The buzz at PAGXX is not very positive on GS FLX+ either. For example, I talked to a core facility head that complained a lot about how their machine didn’t want to run GS FLX+ after the upgrade either. They repeatedly had to have them fixed, or even exchanged. And apparently, they are not the only ones.
I have been, and still are, a big believer in the 454 technology, and have used it successfully for my research. Our core facility has great experience with the instruments and our users are generally very happy with the data. But, the current developments worry me. The niche 454 has always been the longest possible high-throughput (next-gen) reads. But, we, and others, have seen less shotgun projects last year, in favor of long amplicon sequencing, due to the much higher price of 454 sequencing relative to Illumina (and SOLiD). Also, IonTorrent is catching up on read length, with 400 bp coming this year (seeing is believing, though). The PGM, and especially the upcoming Proton instrument, has a troughput that is staggering when you’re used to 454. But also the newly announced upgrade to the MiSeq later this year will get that platform up to 2×250 bases PE sequencing. This means that a 400-450 bp PCR product, currently only sequencable on the 454, can soon easily be done on the MiSeq, at lower cost and higher throughput.
This means that, in principle, the upgrade to GS FLX+ could reinvigorate the interest in this platform, for example for de novo transcriptome and genome sequencing. But the outlook is bleak, at best. Unless GS FLX+ becomes stable all over the world, and reports on the results start becoming very positive, 454 is very fast losing it’s niche to the competitors. To me, it doesn’t look like Roche is taking this situation very seriously. This makes me wonder if they perhaps also have lost faith in 454?
Check out the comments below, and this discussion at SeqAnswers.