On my campus two labs, both with very extensive experience in NGS, have reported that recently purchased Kapa qPCR standards have under-estimated library concentrations. Both sets of libraries were quantified following two similar but lab dependent protocols (one uses the full kit the other uses just the standard and an off the shelf taq-mix) and then diluted to 2 nM and the dilutions were then quantified. Typical amounts of library (10 and 12 pmol/lane; the latter exceeds Illumina's rec. but the group swears by it) were run on HiSeq 8-lane flowcells but produced ~50% of the expected reads (~4x10^8/lane). Typically these labs see 6 - 8 x10^8 reads/lane. One lane contained a sample which was being re-run and was quantified months before with a different lot of Kapa. This recent run of this sample produced the expected number of reads. There was no issue with the quality scores any samples and the data are fine (just lower coverage). The library quantifications were double checked using the suspect Kapa and it doesn't appear to be anything to do with the PCRs.
The dates of purchase and shipping/receiving of the suspect Kapa kits are very similar (Nov 2013) but the lot numbers are different. Has anyone had any trouble with Kapa standards recently?
UPDATE: We spoke to Kapa and they are having problems with lots. I would call ahead before running anything.
The dates of purchase and shipping/receiving of the suspect Kapa kits are very similar (Nov 2013) but the lot numbers are different. Has anyone had any trouble with Kapa standards recently?
UPDATE: We spoke to Kapa and they are having problems with lots. I would call ahead before running anything.
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