Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis

Hosein, Abdel Nasser, Song, Sarah, McCart Reed, Amy E., Jayanthan, Janani, Reid, Lynne E., Kutasovic, Jamie R., Cummings, Margaret C., Waddell, Nic, Lakhani, Sunil R., Chenevix-Trench, Georgia and Simpson, Peter T. (2013) Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis. Laboratory Investigation, 93 6: 701-710. doi:10.1038/labinvest.2013.54

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Author Hosein, Abdel Nasser
Song, Sarah
McCart Reed, Amy E.
Jayanthan, Janani
Reid, Lynne E.
Kutasovic, Jamie R.
Cummings, Margaret C.
Waddell, Nic
Lakhani, Sunil R.
Chenevix-Trench, Georgia
Simpson, Peter T.
Title Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis
Journal name Laboratory Investigation   Check publisher's open access policy
ISSN 0023-6837
Publication date 2013-06
Sub-type Article (original research)
DOI 10.1038/labinvest.2013.54
Open Access Status
Volume 93
Issue 6
Start page 701
End page 710
Total pages 10
Place of publication London, United Kingdom
Publisher Nature Publishing
Collection year 2014
Language eng
Abstract Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples. Owing to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromized, which means obtaining informative data regarding epigenetic, genomic, and expression alterations can be challenging. Here, we have investigated the utility of repairing damaged DNA derived from FFPE tumors prior to single-nucleotide polymorphism (SNP) arrays for whole-genome DNA copy number analysis. DNA was extracted from FFPE samples spanning five decades, involving tumor material obtained from surgical specimens and postmortems. Various aspects of the protocol were assessed, including the method of DNA extraction, the role of Quality Control quantitative PCR (qPCR) in predicting sample success, and the effect of DNA restoration on assay performance, data quality, and the prediction of copy number aberrations (CNAs). DNA that had undergone the repair process yielded higher SNP call rates, reduced log R ratio variance, and improved calling of CNAs compared with matched FFPE DNA not subjected to repair. Reproducible mapping of genomic break points and detection of focal CNAs representing high-level gains and homozygous deletions (HD) were possible, even on autopsy material obtained in 1974. For example, DNA amplifications at the ERBB2 and EGFR gene loci and a HD mapping to 13q14.2 were validated using immunohistochemistry, in situ hybridization, and qPCR. The power of SNP arrays lies in the detection of allele-specific aberrations; however, this aspect of the analysis remains challenging, particularly in the distinction between loss of heterozygosity (LOH) and copy neutral LOH. In summary, attempting to repair DNA that is damaged during fixation and storage may be a useful pretreatment step for genomic studies of large archival FFPE cohorts with long-term follow-up or for understanding rare cancer types, where fresh frozen material is scarce.
Keyword Array CGH
Breast cancer
DNA copy number alterations
DNA restoration
Formalin fixed
Paraffin-embedded tissue
SNP array
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

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Created: Tue, 14 May 2013, 11:26:52 EST by Dr Sarah Song on behalf of Institute for Molecular Bioscience