Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples.
Author(s): Hall JS, Leong HS, Armenoult LS, Newton GE, Valentine HR, Irlam JJ, Möller-Levet C, Sikand KA, Pepper SD, Miller CJ, West CM
Publication: Br J Cancer, 2011, Vol. 104, Page 971-81
PubMed ID: 21407225 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine the effects of diagnosis and storage duration on the RNA expression profiles of cervical cancer specimens. RNA was extracted using RecoverAll, amplified using NuGEN and hybridized to the Exon 1.0 ST array. Data was compared to publically available data from frozen non-small cell lung cancer (NSCLC) specimens hybridized to HG-U133 arrays.
Summary of Findings:
The authors report that specimen age, but not RNA integrity, concentration, or purity, impacted DABG rates, but the data was not shown. Expression profiles of the 28 FFPE specimens clustered based on diagnosis but not storage duration. Using a publicly available dataset of frozen NSCLC specimens, the gene signature generated with FFPE specimens was able to properly classify NSCLC specimens into SCC and AC.
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform RNA DNA microarray DNA Real-time qPCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Frozen
Biospecimen Acquisition Biospecimen location Cervix
Lung
Storage Storage duration 10-16 years
Preaquisition Diagnosis/ patient condition Squamous cell carcinomas
Adenocarcinomas