Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
Covaris FFPE extraction Kit using AFA tubes? Hybridizationx Sample Prep / Library Generation 7 12-01-2014 05:30 AM
Exome sequencing DNA from FFPE tissue JER Illumina/Solexa 4 11-01-2014 08:56 PM
CDNA synthesis from FFPE: best kit/enzyme? BerlindaV Sample Prep / Library Generation 0 08-12-2014 09:45 AM
exome capture kit from Illumina lingfung.tang Sample Prep / Library Generation 1 01-27-2012 04:33 AM
Exome sequencing with Illumina Kit lingfung.tang Illumina/Solexa 5 02-13-2011 10:16 PM

Thread Tools
Old 10-15-2014, 04:50 PM   #1
Amy S
Junior Member
Location: UCSF

Join Date: Oct 2009
Posts: 2
Default 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?
Amy S is offline   Reply With Quote
Old 10-16-2014, 06:35 AM   #2
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.
GW_OK is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:04 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO