MiSeq indexing with Custom Select Oligos

[dcarter]

Hello,
We are using the Nextera Rapid Capture Enrichment kit with Custom Select Oligos to index and equimolar pool 24 samples for a 2x300 PE run on the MiSeq. Every once in a while we have one sample in a pool which has 17%-80% of the reads attributed to that index pair. Has anyone else had this issue? There are many details I have not included in this email, but am willing to provide more details if others have seen this issue, or are willing to offer ideas. We have been working with Illumina for months on this with no solution.
Thanks.

[Ingeneious]

Same index every time?

Possibly the concentration of that index is too high and overly represented? Just throwing out ideas.

[dcarter]

Hello Ingeneious,
No, it is not the same pair of indices that cause the issue, although there are some pairs that cause issues more often than other pairs.