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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed
J S Hall1, H S Leong, L S C Armenoult
1Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
British Journal of Cancer
|March 17, 2011
Summary
Archival formalin-fixed paraffin-embedded (FFPE) tumor samples can yield valuable gene expression data using Exon-array profiling. This method successfully identified distinct gene signatures for cervical cancer subtypes and validated findings in independent datasets.
Area of Science:
- Molecular biology
- Genomics
- Cancer research
Background:
- RNA degradation in formalin-fixed paraffin-embedded (FFPE) samples limits expression profiling.
- Archival FFPE tumor samples are a valuable resource but challenging for molecular analysis.
Purpose of the Study:
- To demonstrate the utility of Exon-array profiling for extracting meaningful gene expression data from archival FFPE tumor samples.
- To derive and validate gene expression signatures from FFPE samples for cancer subtyping.
Main Methods:
- Exon-array profiling of 19 cervical squamous cell carcinoma (SCC) and 9 adenocarcinoma (AC) FFPE samples.
- Validation of derived gene signatures on an independent fresh-frozen non-small cell lung cancer (NSCLC) cohort.
- Gene set enrichment analysis (GSEA) for biological network exploration and Quantigene for differential gene expression confirmation.
Main Results:
- A 1217-gene signature distinguished between SCC and AC in cervical cancer FFPE samples.
- This signature accurately classified 58 independent NSCLC samples into SCC and AC.
- A specific gene network involving hepatic nuclear factor and GATA6 was identified in AC, suggesting a role in cervical glandular cell differentiation.
Conclusions:
- Exon-array profiling of FFPE samples generates robust gene expression signatures applicable to independent datasets.
- This approach enables the identification of novel biological insights and supports the design of assays for platform validation.
- FFPE samples are a viable source for comprehensive gene expression analysis in cancer research.
