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Old 09-04-2014, 08:04 AM   #2
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,232

Does anyone know how well Illumina Hiseq can deal with DNA from FFPE tissue?
HiSeq and other Illumina sequencing systems sequences prepped libraries, so the origin of DNA does not make much difference on sequencer output.

We have a method to deal with the Cytosines changing to Uracil but is it feasible to use DNA from paraffin for exome sequencing if it hasn't degraded too much? We'd be using the Nextera rapid capture Enrichment Kit ideally.
The issue would be preparing a suitable input Nextera library (300 bp peak) for hybridisation step from FFPE tissue DNA as Nextera requires high molecular weight input DNA. A high degree of customisation may be necessary to obtain such library. You might be better off with kits that use short DNA fragments from shearing for library prep step.
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