Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL® sample preparation
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Archived formalin-fixed, paraffin embedded (FFPE) tissues constitute a vast, well-annotated, but underexploited resource for the molecular study of cancer progression, largely because degradation, chemical modification, and cross-linking, render FFPE RNA a suboptimal substrate for conventional analytical methods. We report here a modified protocol for RNA extraction from FFPE tissues which maximized the success rate (with 100% of samples) in the expression profiling of a set of 60 breast cancer samples on the WG-DASL platform; yielding data of sufficient quality such that in hierarchical clustering (a) 12/12 (100%) replicates correctly identified their respective counterparts, with a high self-correlation (r = 0.979), and (b) the overall sample set grouped with high specificity into ER+ (38/40; 95%) and ER− (18/20; 90%) subtypes. These results indicate that a large fraction of decade-old FFPE samples, of diverse institutional origins and processing histories, can yield RNA suitable for gene expression profiling experiments.
KeywordsFFPE RNA extraction WG-DASL Gene expression profiling
This study was supported by funding: NIH/NCI R01CA098858 (KEM, CIL, PLP, LH); Safeway Foundation (PLP, KEM); NIH/NCI P50 CA148143 (PLP). The authors wish to thank Ryan Basom for assistance with use of Bioconductor lumi package, and in data preprocessing.
Conflict of interest
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