As most of you know, we have been unable to run amplicons longer than about 400bp since early 2015. The cause of this was an issue with the Illumina reagents which resulted in a steep drop off in quality of the last 100bp for read 2 on a 2x300 kit. Once we discovered the source of the problem we were forced to move all of the orders already received to a shorter amplicon and restrict new orders to shorter amplicons as well. This of course was not an ideal situation as it reduced the number of variable regions available to sequence, and made it difficult (if not impossible) to compare between orders run on a long amplicon previously.
As you can imagine the whole situation was very frustrating for us as we know it was for many of you. Illumina was pretty accommodating and tried their best to mitigate the negative effects. However, we still had delays and slowdowns because of the situation. The good news is, it looks like we are going to be able to start offering the long chemistry again. In late March we had a conversation with Illumina and they informed us they believed the issue was resolved. We have run two test runs with the updated chemistry and our initial reviews show that the Q-score’s stayed at a consistent level throughout the run with only the normal gradual decline instead of the steep drop off we’d seen all last year. The reads are stitching together well, and we are very optimistic moving forward.
Moving forward we will be accepting orders for longer amplicons (up to 530bp) and have already started running the orders that had been on hold for the longer chemistry. If you’ve done work with us prior to 2015 you know our favorite amplicon is 28F-519R – and now we get to use it again! There will be a period of transition as we move forward. Many of our current orders still require the shorter runs, and to maintain consistency with previous data we will run 2x250 for them. Our plan for the near future is to run one 2x300 run per week as we start transitioning back to longer assays.
If you have questions about the new amplicon options, or just want to know how this will affect you, please don’t hesitate to contact us.