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Oral Cancer
Published in: Oral Cancer 3-4/2019

01-12-2019 | Oral Cancer | Original Article

Identification of stably expressed genes for normalization of gene expression data in oral tumors: a preliminary analysis

Authors: Aniket Parab, Sanit Mhatre, Sujata Hake, Sadhana Kannan, Prathamesh Pai, Shubhada Kane, Narendra Joshi

Published in: Oral Cancer | Issue 3-4/2019

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Abstract

Aim

We sought to identify stably expressed genes in tumors of gingivo-buccal region and tongue from untreated as well as treated patients.

Background

The study was undertaken in view of the ambiguity with regards to the choice of reference genes for normalization of gene expression data from gingivo-buccal region and tongue. This aspect was also examined in tumors from treated patients since it could provide clues for such analyses in the assessment of treatment modalities in the future.

Methods

Expression of ten candidate housekeeping genes, identified in array-based studies, was tested using TaqMan based semi-quantitative real-time PCR. Thirty-five buccal mucosa derived (18 from treated patients) and 15 tongue tumors (8 from treated patients) were studied. Most stable genes were identified based on the consensus between the results of the three methods, Comparative δCt, BestKeeper and NormFinder, used for data analysis.

Results

CHMP2A and VPS29 were identified as the most stably expressed genes suitable for normalization of data from buccal-mucosa tumors, whereas RPS13 and PSMB2 were indicated for similar specimens from treated patients. The same criteria identified stable expression of PSMB2 and PUM1 in tumors from tongue and OAZ1 and RPS13 for the post-treatment tongue tumors.

Conclusion

We have identified stably expressed genes in common oral cancers which can be used for normalization of the gene expression data. Results also established differences in tumors arising at different sites of the oral cavity and highlighted further changes following exposure to therapy.
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Metadata
Title
Identification of stably expressed genes for normalization of gene expression data in oral tumors: a preliminary analysis
Authors
Aniket Parab
Sanit Mhatre
Sujata Hake
Sadhana Kannan
Prathamesh Pai
Shubhada Kane
Narendra Joshi
Publication date
01-12-2019
Publisher
Springer International Publishing
Published in
Oral Cancer / Issue 3-4/2019
Electronic ISSN: 2509-8837
DOI
https://doi.org/10.1007/s41548-019-00020-y