Mass spectrometry-based assay for the molecular diagnosis of glioma: concomitant detection of chromosome 1p/19q codeletion, and IDH1, IDH2, and TERT mutation status.

Chiara Pesenti,Silvana Guerneri,Silvia Tabano,Manuela Caroli,Leda Paganini,Letterio Runza,Monica Miozzo,Stefano Ferrero,Silvano Bosari,Maura Menghi,Laura Fontana,Rosamaria Silipigni,Emanuela Veniani,Giovanni Marfia

doi:10.18632/oncotarget.19103

Chiara Pesenti, Silvana Guerneri + Show 12 more

Open Access

https://doi.org/10.18632/oncotarget.19103

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Abstract

The World Health Organization recently revised the diagnosis of glioma, to integrate molecular parameters, including IDH mutations and codeletion (loss of heterozygosity; LOH) of chromosome arms 1p/19q, into the definitions of adult glioma histological subtypes. Mutations in the TERT promoter may also be useful for glioma diagnosis and prognosis. The integration of molecular markers into routine diagnosis requires their rapid and reliable assessment. We propose a MassARRAY (MS)-based test that can identify 1p/19q codeletion using quantitative SNP genotyping and, simultaneously, characterize hotspot mutations in the IDH1, IDH2, and TERT genes in tumor DNA. We determined the reliability of the MS approach testing 50 gliomas and comparing the MS results with those obtained by standard methods, such as short tandem repeat genotyping, array comparative genomic hybridization (array-CGH) and Fluorescence In Situ Hybridization (FISH) for 1p/19q codeletion and Sanger sequencing for hotspots mutations. The results indicate that MS is suitable for the accurate, rapid, and cost-effective evaluation of chromosome deletions combined with hotspot mutation detection. This MS approach could be similarly exploited in evaluation of LOH in other situations of clinical and/or research importance.

Highlights

Diffuse gliomas are the most common brain tumor, accounting for 27% of all brain neoplasms and 80% of malignant tumors [1]
We determined the reliability of the MS approach testing 50 gliomas and comparing the MS results with those obtained by standard methods, such as short tandem repeat genotyping, array comparative genomic hybridization and Fluorescence In Situ Hybridization (FISH) for 1p/19q codeletion and Sanger sequencing for hotspots mutations
The MS assay optimized in our laboratory is able to reveal Loss of heterozygosity (LOH) at 1p/19q chromosome arms and the presence of hotspot mutations in IDH1, IDH2, and telomerase reverse transcriptase (TERT)

Summary

Introduction

Diffuse gliomas are the most common brain tumor, accounting for 27% of all brain neoplasms and 80% of malignant tumors [1]. At the beginning of 2016, the WHO Classification of Tumors of the Central Nervous System (CNS) (2016 CNS WHO) revised the diagnostic guidelines for gliomas, to include molecular markers and create a novel concept of diagnosis, termed “integrated” diagnosis, characterized by the concomitant evaluation of phenotypic and genotypic parameters [6]. This new integrated diagnostic process aims to achieve greater objectivity, and to improve patient management. IDH mutations promote tumorigenesis by decreasing intracellular levels of NADPH, which has the effect of increasing the sensitivity of tumor cells to cytotoxic therapies, accounting for the positive prognostic value of this marker (see [10] for a review)

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