Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours.
Author(s): Linton KM, Hey Y, Saunders E, Jeziorska M, Denton J, Wilson CL, Swindell R, Dibben S, Miller CJ, Pepper SD, Radford JA, Freemont AJ
Publication: Br J Cancer, 2008, Vol. 98, Page 1403-14
PubMed ID: 18382428 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 preservation method on microarray analysis of RNA in soft tissue sarcomas, lipomas and leiomyomas and to compare results with real-time PCR analysis. FFPE tissues had been stored for 1-8 years prior to the study.
Summary of Findings:
The percent present calls for the two frozen specimens were 49% and 53%, while the corresponding FFPE specimens had percent present calls of 27% and 28%. Only 3-4% of probes hybridized only to FFPE specimens, indicating a high degree of specificity. Expression of abundant transcripts was similar between FFPE and frozen specimens, but for transcripts with a real-time PCR cycle threshold (CT) above thirty for frozen specimens, detection of the FFPE transcript was poor. Generally a high level of agreement between microarray and real-time PCR results was observed for highly expressed genes and genes for which a consistent fold change was observed, but when a different region of the transcript was assayed, the agreement diminished, and in some cases, the direction of change differed. The authors report that FFPE specimens were able to be used to identify genes that may increase the risk of metastasis or mortality.
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Sarcoma
- Neoplastic - Benign
Platform:
Analyte Technology Platform RNA DNA microarray RNA Real-time qRT-PCR Protein Immunohistochemistry Protein Tissue microarray Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Frozen
DNA microarray Specific Technology platform Real-time PCR
Immunohistochemistry Specific Targeted peptide/protein TRKB
CMET
Real-time qRT-PCR Specific Targeted nucleic acid RECQL4
FRRS1
CFH
MET
Preaquisition Diagnosis/ patient condition Leiomyosarcoma
Liposarcoma
Synovial sarcoma
Lipomas
Leiomyomas