Reference genes for gene expression analysis by real-time reverse transcription polymerase chain reaction of renal cell carcinoma

Diagn Mol Pathol. 2011 Dec;20(4):212-7. doi: 10.1097/PDM.0b013e318212e0a9.


Background: Differentiation between malignant renal cell carcinoma and benign oncocytoma is of great importance to choose the optimal treatment. Accurate preoperative diagnosis of renal tumor is therefore crucial; however, existing imaging techniques and histologic examinations are incapable of providing an optimal differentiation profile. Analysis of gene expression of molecular markers is a new possibility but relies on appropriate standardization to compare different samples. The aim of this study was to identify stably expressed reference genes suitable for the normalization of results extracted from gene expression analysis of renal tumors.

Methods: Expression levels of 8 potential reference genes (ATP5J, HMBS, HPRT1, PPIA, TBP, 18S, GAPDH, and POLR2A) were examined by real-time reverse transcription polymerase chain reaction in tumor and normal tissue from removed kidneys from 13 patients with renal cell carcinoma and 5 patients with oncocytoma.

Results: The expression levels of genes were compared by gene stability value M, average gene stability M, pairwise variation V, and coefficient of variation CV. More candidates were not suitable for the purpose, but a combination of HMBS, PPIA, ATP5J, and TBP was found to be the best combination with an average gene stability value M of 0.9 and a CV of 0.4 in the 18 tumors and normal tissues.

Conclusions: A combination of 4 genes, HMBS, PPIA, ATP5J, and TBP, is a possible reference in renal tumor gene expression analysis by reverse transcription polymerase chain reaction. A combination of four genes, HMBS, PPIA, ATP5J and TBP, being stably expressed in tissues from RCC is possible reference genes for gene expression analysis.

MeSH terms

  • Adenoma, Oxyphilic / diagnosis*
  • Adenoma, Oxyphilic / genetics
  • Biomarkers, Tumor / analysis
  • Biomarkers, Tumor / genetics
  • Carcinoma, Renal Cell / diagnosis*
  • Carcinoma, Renal Cell / genetics
  • Diagnosis, Differential
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Kidney Neoplasms / diagnosis*
  • Kidney Neoplasms / genetics
  • RNA, Neoplasm / analysis
  • RNA, Neoplasm / genetics
  • RNA, Neoplasm / isolation & purification
  • Real-Time Polymerase Chain Reaction*
  • Reference Standards
  • Reverse Transcriptase Polymerase Chain Reaction*


  • Biomarkers, Tumor
  • RNA, Neoplasm

Supplementary concepts

  • Oncocytoma, renal