Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample preparation.

Publication Type:

Journal Article


Breast cancer research and treatment, Volume 125, Issue 3, p.879-83 (2011)


2011, Breast, Breast Neoplasms, Center-Authored Paper, Cluster Analysis, Cohort Studies, Estrogen Receptor alpha, Female, Formaldehyde, Gene Expression Profiling, GENOMICS, Human Biology Division, Humans, Immunohistochemistry, Paraffin Embedding, Public Health Sciences Division, Research Trials Office Core Facility - Biostatistics Service, Reverse Transcriptase Polymerase Chain Reaction, RNA, Neoplasm, Shared Resources


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.