We just had a suboptimal run on our 454 intrument in which the modal read length was closer to 200 bp than 400 bp. We are relative newcomers to the game, so our first thoughts were that we had done something wrong. But after racking our brains, we couldn’t think of anything, so we presented all our data to Roche and were a bit surprised when they offered to replace the kit without any quibbling. Then we received a message saying that the delivery for an order for more kits was going to delayed for three weeks 
At first, we didn’t make a connection between the two problems, but several other sequencing centres have also been experiencing similar problems, so one has to assume that Roche has had a problem with their production line, which would also provide the most parsimonious explanation for the supply problem. I have to say we are disappointed here in Birmingham that Roche have not been upfront about this issue, particularly as it is unclear what has been causing the problem and whether it is ongoing or has been sorted. And the cynic in me worries that small users like us are last in the queue, behind all the big centres, when new batches of acceptable reagents come off the production line.
What is also troubling is the idea that a lot of other small centres are also suffering in silence with this issue, not realising that poor performance is nothing to do with anything they have or have not done wrong.
Don’t get me wrong—I think 454 is a wonderful technology that makes things possible that we could have only dreamt about a few years ago! But on this issue, Roche could easily go from heroes to zeroes pretty quickly. And in case you wouldn’t expect full disclosure from them, check out this article from Wired from a few years back: http://www.wired.com/wired/archive/15.04/wired40_ceo.html
If you too have been suffering in silence, drop us a comment to let us know! And Roche, if you want to let the world know what’s going on, feel free to add a comment.
yes… well we have been told its fluidics… But we think its chemistry… or at least chemistry as well.
thanks for sharing
By the way please all come to the UK NExt Gen meeting in Nottingham on August 12th/13th in Nottingham. I’ll send out information about it at the beginning of April
Just for the record our most recent delivery and run went OK, which is reassuring. But the lingering anxiety that the problems might recur remains. If any other readers continue to experience similar problems, please let us know.
Illumina too have suffered problems. We have just had to replace our system entirely due to a bizzare fault Illumina were unable to diagnose. Read lengths beyond 36bp seemed to cause loss of focus issues which could not be rectified despite a complete overhaul by engineers.
Illumina have been good in providing capacity for us at a facility to help clear our backlog and supplied a loan machine in the meantime, but time is money…
[...] timely and reassuring (though in a sad way) post from Mark Pallen (”Experiencing suboptimal 454 runs and slow Roche deliveries? You are not [...]
Again, to set the record straight, this issue has now been resolved completely to our satisfaction. The defective kits have been replaced, we have received a copy of a letter from Christopher McLeod, CEO of 454 Life Sciences, apologising from the problems and Roche are now making a commitment to hold stock in a UK warehouse to provide a buffer against global stocking issues. And we continue to be excited with the great research we can do on the 454 platform!
Now, if you want to hear a real tale of woe, ask the guys at the University of Exeter to tell you about the problems with their defective Illumina instrument, which was eventually replaced with a new instrument! But as Konrad Paszkiewicz said at yesterday’s Sequencing South West meeting, “now everyone can have their own virtual sanger centre”, so let’s remember that when they work, these technologies are just fantastic!