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TP53 mutation analysis in chronic lymphocytic leukemia: comparison of different detection methods

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Tumor Biology

Abstract

TP53 gene defects represent a strong adverse prognostic factor for patient survival and treatment resistance in chronic lymphocytic leukemia (CLL). Although various methods for TP53 mutation analysis have been reported, none of them allow the identification of all occurring sequence variants, and the most suitable methodology is still being discussed. The aim of this study was to determine the limitations of commonly used methods for TP53 mutation examination in CLL and propose an optimal approach for their detection. We examined 182 CLL patients enriched for high-risk cases using denaturing high-performance liquid chromatography (DHPLC), functional analysis of separated alleles in yeast (FASAY), and the AmpliChip p53 Research Test in parallel. The presence of T53 gene mutations was also evaluated using ultra-deep next generation sequencing (NGS) in 69 patients. In total, 79 TP53 mutations in 57 (31 %) patients were found; among them, missense substitutions predominated (68 % of detected mutations). Comparing the efficacy of the methods used, DHPLC and FASAY both combined with direct Sanger sequencing achieved the best results, identifying 95 % and 93 % of TP53-mutated patients. Nevertheless, we showed that in CLL patients carrying low-proportion TP53 mutation, the more sensitive approach, e.g., ultra-deep NGS, might be more appropriate. TP53 gene analysis using DHPLC or FASAY is a suitable approach for mutation detection. Ultra-deep NGS has the potential to overcome shortcomings of methods currently used, allows the detection of minor proportion mutations, and represents thus a promising methodology for near future.

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Acknowledgments

The authors would like to thank ERIC steering board for support, Hana Skuhrova-Francova, Lenka Jurackova and Jitka Kabathova for help with experimental analysis and Matthew Smith for language editing. This study was supported by VaVPI project MSMT CR CZ.1.05/1.1.00/02.0068 of Central European Institute of Technology (CEITEC) and projects of the Internal Grant Agency, Ministry of Health, Czech Republic IGA MZ CR NT13493-4/2012 and NT13519-4/2012.

Conflict of interest

The authors declare that they have no conflict of interests. Sim Truong and Nancy Patten are employed by Roche Molecular Systems, Inc.

Author information

Authors and Affiliations

  1. Central European Institute of Technology (CEITEC), Masaryk University Brno, Kamenice 5, CZ-625 00, Brno, Czech Republic

    Barbara Kantorova, Jitka Malcikova, Sarka Pavlova, Martin Trbusek, Nikola Tom, Karla Plevova, Boris Tichy, Jana Kotaskova, Michael Doubek, Jiri Mayer & Sarka Pospisilova

  2. Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, Cernopolni 9, CZ-613 00, Brno, Czech Republic

    Barbara Kantorova, Jitka Malcikova, Sarka Pavlova, Martin Trbusek, Karla Plevova, Eva Diviskova, Alexandra Oltova, Yvona Brychtova, Michael Doubek, Jiri Mayer & Sarka Pospisilova

  3. Department of Pathology, University Hospital Brno, Jihlavska 20, CZ-625 00, Brno, Czech Republic

    Jana Smardova

  4. Roche Molecular Systems, Inc., 4300 Hacienda Drive, Pleasanton, CA, 94588, USA

    Sim Truong & Nancy Patten

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  1. Barbara Kantorova
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Corresponding author

Correspondence to Sarka Pospisilova.

Additional information

Barbara Kantorova and Jitka Malcikova contributed equally to this study

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Kantorova, B., Malcikova, J., Smardova, J. et al. TP53 mutation analysis in chronic lymphocytic leukemia: comparison of different detection methods. Tumor Biol. 36, 3371–3380 (2015). https://doi.org/10.1007/s13277-014-2971-0

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  • DOI: https://doi.org/10.1007/s13277-014-2971-0

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