Illumina support when switching to kits from another vendor?

[cknox]

I have a question for the forum. If you have an Illumina platform and have chosen to switch from Illumina-manufactured library kits (TruSeq or Nextera) to another vendor's kits, have you seen a negative response from Illumina? Have you had issues with getting support after switching? If so, what happened, and how did you deal with it?

[ECO]

Their first questions/assumptions have always been related to sample prep methods, indexing, etc, even when our instruments are clearly not performing (we don't use their sample prep kits, but prep large #s of samples in a nearly fully automated workflow).

For the first months of issues, I had to show (or discuss) lots of sample QC metrics before they were comfortable enough with our sample prep prowess that they would stop asking me about the sample prep when the instrument clearly didn't focus. Sending them our trending reports across hundred+ MiSeq runs was helpful to convince them.

I know this isn't really an anecdote about switching away from Truseq...but in my opinion (having been in a NGS sample prep customer support-ish role), Illumina has every right to question users that choose to move away from the validated path. Reagent companies could produce a sub-par product, and a large fraction of users don't understand (or overlook) some of the consequences to their sample-prep actions...so it makes instrument support kind of a nightmare if the input material is suspect.

Illumina was never overtly or even subtly negative about the fact that we homebrew everything...they were approaching the support as they should: ruling out garbage-in/garbage-out before they suspect other things.

[cknox]

Eco - this make sense. I too have acted in a customer technical support role and Illumina is certainly right to ask questions. The issue is more around not offering support at all or delaying support due to the customer not using their kits. Have you or others seen issues like this?