Hi everyone,
I'm looking for some advice from anyone who has used Illumina's FFPE QC kit to determine DNA quality from their FFPE samples. From what I can gather, the kit runs long range qPCRs, and the Ct of each sample, compared to the Ct of the Illumina provided standard template, gives you an idea of how degraded your sample is.
Illumina give suggested cut-offs for their various protocols (sampleCt - standardCt<5 is good for methylation assay; sampleCt - standardCt<2 is good for the cancer panel library prep.).
My questions is does anyone have any experience of running this kit and trying the samples for exome capture? Or indeed any other assay. I want more of an idea of the samples I can get away with. Could I use a sample with a deltaCt of 2.1 and expect decent results?
I'm looking for some advice from anyone who has used Illumina's FFPE QC kit to determine DNA quality from their FFPE samples. From what I can gather, the kit runs long range qPCRs, and the Ct of each sample, compared to the Ct of the Illumina provided standard template, gives you an idea of how degraded your sample is.
Illumina give suggested cut-offs for their various protocols (sampleCt - standardCt<5 is good for methylation assay; sampleCt - standardCt<2 is good for the cancer panel library prep.).
My questions is does anyone have any experience of running this kit and trying the samples for exome capture? Or indeed any other assay. I want more of an idea of the samples I can get away with. Could I use a sample with a deltaCt of 2.1 and expect decent results?
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