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The use of the Illumina FFPE Restoration Protocol to obtain suitable quality DNA for SNP-based CGH– a pilot study

BioMed Central
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DOI: 10.1186/1897-4287-10-s2-a85
  • Meeting Abstract


MEETING ABSTRACT Open Access The use of the Illumina FFPE Restoration Protocol to obtain suitable quality DNA for SNP-based CGH– a pilot study AN Hosein1,2*, S Cocciardi1, J Jayanthan2, S Song2, P Simpson2, G Chenevix-Trench1,2 From Familial Aspects of Cancer 2011 Research and Practice: A combined meeting of kConFab, Australian Breast Cancer Family Study, Australian Colorectal Cancer Family Study, Australian Ovarian Cancer Study, Family Cancer Clinics of Australia and New Zealand and kConFab Kingscliff, Australia. 23-26 August 2011 The use of formalin fixed paraffin embedded (FFPE) tis- sues for DNA analysis has been met with great difficul- ties due to the degradative effect this fixation, processing and storage has on DNA quality. The lack of a suitable protocol to enhance the quality of such degraded DNA has been a great hindrance to our ability to make full use of clinically annotated FFPE cancer tis- sue banks. In this report we have begun to investigate the effectiveness and limitations to Illumina’s recent platform for the restoration of DNA derived from archi- val FFPE tissues. With the exception of select fresh frozen and blood samples, all DNA samples were extracted from FFPE tis- sues and restored according to Illumina’s protocol. The quality of the FFPE extracted DNA was then assessed by Illumina’s PCR-based quality control assay (QC-PCR) and the resultant DNA was subsequently run on Illumi- na’s SNP-based CGH chips. Chip call rates were largely used in order to determine the quality of a particular array. Overall, the chip data were highly reproducible as determined by comparing several technical replicate samples. FFPE-extracted and restored DNA performed well in comparison to DNA extracted from fresh frozen tumor and blood from the same patients, meeting the minimum standard for continuation of this platform. It should also be noted that the quality of the chip data was not appreciably enhanced by the use of sodium thiocyanate during the extraction of DNA from FFPE tissu

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