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| Status |
Public on Aug 03, 2011 |
| Title |
A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Samples were prospectively collected from patients with histologically normal surgical resection margins. 96 tissue samples (histologically normal margins, oral carcinoma and adjacent normal tissues) from 24 patients comprised the training set. Our study design was guided by the hypothesis that the expression of genes present in oral squamous cell carcinoma (OSCC) but not in healthy oral tissues would be indicative of recurrence in advance of histological alteration. We used meta-analysis of five published microarray data sets (GEO accession GDS2520, Kuriakose et al. 2004; GDS1584, Toruner et al. 2004; GSE6791, Pyeon et al. 2007; GSE9844, Ye et al. 2008; and GSE10121, Sticht et al. 2008), in conjunction with the current training set, to identify genes reliably over-expressed in OSCC. This reduced gene set was used to train a risk model to predict recurrence based on over-expression of a subset of these genes in histologically normal surgical resection margins. Validation of the risk signature was performed using quantitative real-time reverse-transcription PCR in an independent set of 136 samples from an independent cohort of 30 patients.
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| Overall design |
This was a case-only design involving a training set of 23 tumors and 73 margins from 24 patients with squamous cell carcinoma of the tongue.
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| Contributor(s) |
Reis PP, Waldron L, Perez-Ordonez B, Pintilie M, Galloni NN, Xuan Y, Cervigne NK, Warner GC, Makitie AA, Simpson C, Goldstein D, Brown D, Gilbert R, Gullane P, Irish J, Jurisica I, Kamel-Reid S |
| Citation(s) |
21989116 |
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| Submission date |
Jul 29, 2011 |
| Last update date |
Oct 16, 2012 |
| Contact name |
Levi Waldron |
| E-mail(s) |
[email protected]
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| Organization name |
Harvard School of Publich Health
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| Department |
Biostatistics
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| Street address |
655 Huntington Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL10526 |
[HG-U133_Plus_2] Affymetrix GeneChip Human Genome HG-U133 Plus 2 Array [Brainarray HGU133Plus2_Hs_ENTREZG_v12] |
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| Samples (96)
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| Relations |
| BioProject |
PRJNA144853 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31056_RAW.tar |
457.0 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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