Illumina FFPE QC Kit for exome sequencing

Amy S · 10-15-2014, 04:50 PM

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?

GW_OK · 10-16-2014, 06:35 AM

We've used the Kappa hgDNA QC kit on FFPE samples. Can't recall exactly what the data looked like but the numbers were below what their protocol said was good quality DNA. Saved us some money on what would have been a dead end project.

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10-15-2014, 04:50 PM	#1
Amy S Junior Member Location: UCSF Join Date: Oct 2009 Posts: 2	Illumina FFPE QC Kit for exome sequencing 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?

10-16-2014, 06:35 AM	#2
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 411	We've used the Kappa hgDNA QC kit on FFPE samples. Can't recall exactly what the data looked like but the numbers were below what their protocol said was good quality DNA. Saved us some money on what would have been a dead end project.