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Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

Author

Listed:
  • Ward De Spiegelaere
  • Jutta Dern-Wieloch
  • Roswitha Weigel
  • Valérie Schumacher
  • Hubert Schorle
  • Daniel Nettersheim
  • Martin Bergmann
  • Ralph Brehm
  • Sabine Kliesch
  • Linos Vandekerckhove
  • Cornelia Fink

Abstract

Background: An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results: 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions: This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use.

Suggested Citation

  • Ward De Spiegelaere & Jutta Dern-Wieloch & Roswitha Weigel & Valérie Schumacher & Hubert Schorle & Daniel Nettersheim & Martin Bergmann & Ralph Brehm & Sabine Kliesch & Linos Vandekerckhove & Cornelia, 2015. "Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages," PLOS ONE, Public Library of Science, vol. 10(3), pages 1-13, March.
    • Handle: RePEc:plo:pone00:0122515
    DOI: 10.1371/journal.pone.0122515
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    Cited by:

    1. Nirmal Kumar Sampathkumar & Venkat Krishnan Sundaram & Prakroothi S Danthi & Rasha Barakat & Shiden Solomon & Mrityunjoy Mondal & Ivo Carre & Tatiana El Jalkh & Aïda Padilla-Ferrer & Julien Grenier & , 2022. "RNA-Seq is not required to determine stable reference genes for qPCR normalization," PLOS Computational Biology, Public Library of Science, vol. 18(2), pages 1-24, February.

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