scholarly journals A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5207 ◽  
Author(s):  
Vinayak Palve ◽  
Manisha Pareek ◽  
Neeraja M. Krishnan ◽  
Gangotri Siddappa ◽  
Amritha Suresh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Head And Neck ◽  
Internal Control ◽  
Head And Neck Tumor ◽  
Multiple Sources ◽  
Minimal Set ◽  
Neck Tumor ◽  
Expression Studies ◽  
Internal Control Genes ◽  
Gene Expression Studies

Selection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. The aim of the present study was to discover and validate a minimal set of internal control genes in head and neck tumor studies. We analyzed data from multiple sources (in house whole-genome gene expression microarrays, previously published quantitative real-time PCR (qPCR) data and RNA-seq data from TCGA) to come up with a list of 18 genes (discovery set) that had the lowest variance, a high level of expression across tumors, and their matched normal samples. The genes in the discovery set were ranked using four different algorithms (BestKeeper, geNorm, NormFinder, and comparative delta Ct) and a web-based comparative tool, RefFinder, for their stability and variance in expression across tissues. Finally, we validated their expression using qPCR in an additional set of tumor:matched normal samples that resulted in five genes (RPL30, RPL27, PSMC5, MTCH1, and OAZ1), out of which RPL30 and RPL27 were most stable and were abundantly expressed across the tissues. Our data suggest that RPL30 or RPL27 in combination with either PSMC5 or MTCH1 or OAZ1 can be used as a minimal set of control genes in head and neck tumor gene expression studies.

scholarly journals A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

2017 ◽  
Author(s):  
Vinayak Palve ◽  
Manisha Pareek ◽  
Neeraja M Krishnan ◽  
Gangotri Siddappa ◽  
Amritha Suresh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Head And Neck Cancer ◽  
Head And Neck ◽  
Internal Control ◽  
Minimal Set ◽  
Normal Tissues ◽  
Neck Tumors ◽  
Expression Studies ◽  
Internal Control Genes ◽  
Gene Expression Studies

AbstractBackgroundSelection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. In head and neck cancer, studies evaluating the efficacy of internal reference genes are rare. Here, we present data for a minimal set of candidates as internal control genes for gene expression studies in head and neck cancer.MethodsWe analyzed data from multiple sources (in house whole-genome gene expression microarrays, n=21; TCGA RNA-seq, n=42, and published gene expression studies in head and neck tumors from literature) to come up with a set of genes (discovery set) for their stable expression across tumor and normal tissues. We then performed independent validation of their expression using qPCR in 14 tumor:normal pairs. Genes in the discovery set were ranked using four different algorithms (BestKeeper, geNorm, NormFinder, and comparative delta Ct) and a web-based comparative tool, RefFinder, for their stability and variance in expression across tissues.ResultsOur analyses resulted in 18 genes (discovery set) that had lowest variance and high level of expression across tumor and normal samples. Independent experimental validation and analyses with multiple tools resulted in top ranked five genes (RPL30, RPL27, PSMC5, OAZ1 and MTCH1) out of which, RPL30 (60S ribosomal protein L30) and RPL27 (60S ribosomal protein L27), performed best and were abundantly expressed across tumor and normal tissues.ConclusionsRPL30 and RPL27 are stably expressed in HNSCC and should be used as internal control genes in gene expression in head and neck tumors studies.

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