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Development of a Rapid and Sensitive IDH1/2 Mutation Detection Method for Glial Tumors and a Comparative Mutation Analysis of 236 Glial Tumor Samples

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Abstract

Background

The presence of mutations in the isocitrate dehydrogenase 1 and 2 genes (IDH1/2) in glioma tumors is correlated with good prognosis upon standard-of-care treatment. Therefore, information on whether the glioma tumor has IDH1/2 mutations could be used in the correct diagnosis and management of glial tumors. The two most common techniques used to detect IDH1/2 mutations, immunohistochemistry (IHC) and Sanger sequencing, are prone to missing these mutations, especially if the tumor cells that carry the mutations constitute a small minority of the tumor itself.

Objectives

We developed and validated a rapid method (3-mismatch-amplification refractory mutation system [3m-ARMS]) that can be used for pre-, intra- and postoperative detection of the most common IDH1/2 mutations in glial tumors with high specificity and sensitivity. We also conducted a comprehensive IDH1/2 mutation analysis in 236 glial tumor samples comparing 3m-ARMS, IHC and Sanger sequencing.

Methods

3m-ARMS was optimized and validated for the specific and sensitive detection of the most common IDH1 and IDH2 mutations. We then analyzed 236 glial tumor samples for the presence of IDH1/2 mutations using 3m-ARMS, Sanger sequencing and IHC techniques. We then analyzed and compared the results, evaluating the diagnostic and screening potential of 3m-ARMS.

Results

Comparison of the three techniques used in the mutation analysis showed that 3m-ARMS-based IDH1/2 mutation detection was superior to IHC and Sanger sequencing-based IDH1/2 mutation detection in terms of accuracy, specificity and sensitivity, especially for tumor samples in which only a small minority of the cell population carried the mutation. 3m-ARMS could detect the presence of femtogram levels of IDH1/2 mutant DNA in DNA samples in which the mutant DNA-to-wild-type DNA ratio was as low as 1:100,000.

Conclusion

Sanger sequencing and IHC-based methods have shortcomings when detecting mutations in glial tumors so can miss IDH1/2 mutations in glial tumors when used alone without proper modifications. 3m-ARMS-based mutation detection is fast and simple with potential for use as a diagnostic test for the majority of hot spot mutations in IDH1/2 genes. It can detect IDH1/2 mutations within an hour so can be adapted for intraoperative diagnosis.

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Authors and Affiliations

  1. Department of Medical Biology, School of Medicine, Bahcesehir University, Sahrayicedid Mah. Batman Sok, No: 66 Kadikoy, Istanbul, 34734, Turkey

    Timucin Avsar, Melih Acar & Turker Kilic

  2. Neuroscience Program, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey

    Timucin Avsar, Alihan Sursal, Gizem Turan, Berfu Nur Yigit, Deniz Altunsu & Turker Kilic

  3. Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey

    Timucin Avsar, Alihan Sursal, Gizem Turan, Berfu Nur Yigit, Deniz Altunsu, Kutay Cantasir, Gözde Duyu, Melih Acar & Turker Kilic

  4. Department of Neurosurgery, School of Medicine, Bahcesehir University, Istanbul, Turkey

    Ahmed B. Bayoumi & Turker Kilic

  5. Division of Neurosurgery, Department of Surgery, McMaster University, Hamilton, ON, Canada

    Ahmed B. Bayoumi

  6. Department of Pathology, School of Medicine, Bahcesehir University, Istanbul, Turkey

    Ozlem Yapicier

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  1. Timucin Avsar
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Contributions

TA and MA conceived and designed the study and wrote the manuscript. AS, GT, BNY, DA, KC, GD, AB, OY participated in data acquisition, analysis and interpretation of data. TK provided the tumor samples and patient information and participated in critical discussions.

Corresponding authors

Correspondence to Timucin Avsar, Melih Acar or Turker Kilic.

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Conflicts of interest

Timucin Avsar, Alihan Sursal, Gizem Turan, Berfu Nur Yigit, Deniz Altunsu, Kutay Cantasir, Gözde Duyu, Ahmed Bayoumi, Ozlem Yapicier, Melih Acar, and Turker Kilic have no conflicts of interest that are directly relevant to the content of this article.

Funding

This study was funded by Bahcesehir University, Scientific Research Projects Council, project no. BAP.2018-2.01, and The Scientific and Technological Research Council of Turkey (TUBITAK) Grant, project no. 118S539.

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Avsar, T., Sursal, A., Turan, G. et al. Development of a Rapid and Sensitive IDH1/2 Mutation Detection Method for Glial Tumors and a Comparative Mutation Analysis of 236 Glial Tumor Samples. Mol Diagn Ther 24, 327–338 (2020). https://doi.org/10.1007/s40291-020-00461-y

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  • DOI: https://doi.org/10.1007/s40291-020-00461-y

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