Exon-array profiling unlocks clinically and biologically relevant gene signatures from @entity406 -fixed paraffin-embedded XXXX samples.

@entity43289 @entity5 @entity957 @entity1149 @entity406 @entity982 @entity420
BACKGROUND: Degradation and chemical modification of RNA in @entity406 -fixed @entity982 -embedded (FFPE) samples hamper their use in expression profiling studies. This study aimed to show that useful information can be obtained by Exon-array profiling @entity5 samples. METHODS: Nineteen cervical @entity957 ( @entity957 ) and 9 @entity420 ( @entity420 ) FFPE samples (10-16-year-old) were profiled using Affymetrix Exon arrays. The gene signature derived was tested on a fresh-frozen @entity1149 ( @entity1149 ) series. Exploration of biological networks involved gene set enrichment analysis (GSEA). Differential gene expression was confirmed using Quantigene, a multiplex bead-based alternative to qRT-PCR. RESULTS: In all, 1062 genes were higher in @entity957 vs @entity420 , and 155 genes higher in @entity420 . The 1217-gene signature correctly separated 58 @entity1149 into @entity957 and @entity420 . A gene network centered on hepatic nuclear factor and @entity43289 was identified in @entity420 , suggesting a role in glandular cell differentiation of the cervix. Quantigene analysis of the top 26 differentially expressed genes correctly partitioned cervix samples as @entity957 or @entity420 . CONCLUSION: FFPE samples can be profiled using Exon arrays to derive gene expression signatures that are sufficiently robust to be applied to independent data sets, identify novel biology and design assays for independent platform validation.
