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| Status |
Public on Feb 17, 2011 |
| Title |
Exon-array profiling of squamous cell carcinoma and adenocarcinoma in human cervical FFPE samples |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. In this study, we investigated the feasibility of gene expression signature generation from archival FFPE materials. Nineteen cervical squamous cell carcinoma (SCC) and nine adenocarcinoma (AC) 10~16-year-old FFPE samples were profiled using Affymetrix Exon 1.0 ST arrays. A comparison of the global gene expression changes between SCC and AC revealed 1217 differentially expressed genes. Of these, 1062 showed significantly higher expression levels in SCC relative to AC, and 155 genes were found to be specifically upregulated in AC. When the 1217-gene signature was tested on a fresh-frozen human non-small cell lung cancer (NSCLC) series, it correctly separated the 58 NSCLC samples into SCC and AC. In conclusion, our results showed that clinically and biologically relevant gene expression profiles can be derived from FFPE samples with Exon array profiling.
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| Overall design |
The study population contains 28 FFPE human cervix samples (19 SCC and 9 AC). Histopathology assessment and p63 IHC were performed on all samples to confirm their histological subtypes. Total RNA was extracted and hybridised to Affymetrix Human Exon 1.0 ST arrays. Expression values were normalised using RMA. Only exonic probesets that were flagged as present (DABG< 0.01) in at least three samples were retained for further analysis. LIMMA was used to identify probesets that were differentially expressed between SCC and AC subtypes, using FDR ≤ 0.01 and absolute fold-change ≥ 2 as cutoff.
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| Contributor(s) |
Hall JS, Leong HS, Armenoult LS, Newton GE, Valentine HR, Irlam JJ, Möller-Levet C, Sikand KA, Pepper SD, Miller CJ, West CM |
| Citation(s) |
21407225 |
| Submission date |
Feb 17, 2011 |
| Last update date |
Jul 10, 2014 |
| Contact name |
Hui Sun Leong |
| E-mail(s) |
HuiSun.Leong@cruk.manchester.ac.uk
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| Organization name |
Cancer Research UK Manchester Institute
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| Department |
The University of Manchester
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| Lab |
Computational Biology Support Team
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| Street address |
Wilmslow Road
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| City |
Manchester |
| ZIP/Postal code |
M20 4BX |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL5188 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [probe set (exon) version] |
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| Samples (28)
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| GSM677289 |
squamous cell carcinoma, biological replicate 1 |
| GSM677290 |
squamous cell carcinoma, biological replicate 2 |
| GSM677291 |
squamous cell carcinoma, biological replicate 3 |
| GSM677292 |
squamous cell carcinoma, biological replicate 4 |
| GSM677293 |
squamous cell carcinoma, biological replicate 5 |
| GSM677294 |
squamous cell carcinoma, biological replicate 6 |
| GSM677295 |
squamous cell carcinoma, biological replicate 7 |
| GSM677296 |
squamous cell carcinoma, biological replicate 8 |
| GSM677297 |
squamous cell carcinoma, biological replicate 9 |
| GSM677298 |
squamous cell carcinoma, biological replicate 10 |
| GSM677299 |
squamous cell carcinoma, biological replicate 11 |
| GSM677300 |
squamous cell carcinoma, biological replicate 12 |
| GSM677301 |
squamous cell carcinoma, biological replicate 13 |
| GSM677302 |
squamous cell carcinoma, biological replicate 14 |
| GSM677303 |
squamous cell carcinoma, biological replicate 15 |
| GSM677304 |
squamous cell carcinoma, biological replicate 16 |
| GSM677305 |
squamous cell carcinoma, biological replicate 17 |
| GSM677306 |
adenocarcinoma, biological replicate 1 |
| GSM677307 |
adenocarcinoma, biological replicate 2 |
| GSM677308 |
adenocarcinoma, biological replicate 3 |
| GSM677309 |
adenocarcinoma, biological replicate 4 |
| GSM677310 |
adenocarcinoma, biological replicate 5 |
| GSM677311 |
squamous cell carcinoma, biological replicate 18 |
| GSM677312 |
adenocarcinoma, biological replicate 6 |
| GSM677313 |
adenocarcinoma, biological replicate 7 |
| GSM677314 |
squamous cell carcinoma, biological replicate 19 |
| GSM677315 |
adenocarcinoma, biological replicate 8 |
| GSM677316 |
adenocarcinoma, biological replicate 9 |
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| Relations |
| BioProject |
PRJNA137011 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE27388_RAW.tar |
611.6 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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