Molecular Diagnosis of Diffuse Gliomas through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid

Abstract

Purpose: Diffuse gliomas are the most common primary tumor of the brain and include different subtypes with diverse prognosis. The genomic characterization of diffuse gliomas facilitates their molecular diagnosis. The anatomical localization of diffuse gliomas complicates access to tumor specimens for diagnosis, in some cases incurring high-risk surgical procedures and stereotactic biopsies. Recently, cell-free circulating tumor DNA (ctDNA) has been identified in the cerebrospinal fluid (CSF) of patients with brain malignancies. Experimental Design: We performed an analysis of IDH1, IDH2, TP53, TERT, ATRX, H3F3A, and HIST1H3B gene mutations in two tumor cohorts from The Cancer Genome Atlas (TCGA) including 648 diffuse gliomas. We also performed targeted exome sequencing and droplet digital PCR (ddPCR) analysis of these seven genes in 20 clinical tumor specimens and CSF from glioma patients and performed a histopathologic characterization of the tumors. Results: Analysis of the mutational status of the IDH1, IDH2, TP53, TERT, ATRX, H3F3A, and HIST1H3B genes allowed the classification of 79% of the 648 diffuse gliomas analyzed, into IDH-wild-type glioblastoma, IDH-mutant glioblastoma/diffuse astrocytoma and oligodendroglioma, each subtype exhibiting diverse median overall survival (1.1, 6.7, and 11.2 years, respectively). We developed a sequencing platform to simultaneously and rapidly genotype these seven genes in CSF ctDNA allowing the subclassification of diffuse gliomas. Conclusions: The genomic analysis of IDH1, IDH2, TP53, ATRX, TERT, H3F3A, and HIST1H3B gene mutations in CSF ctDNA facilitates the diagnosis of diffuse gliomas in a timely manner to support the surgical and clinical management of these patients. Clin Cancer Res; 24(12); 2812–9. ©2018 AACR.

Beyond the Blood: CSF-Derived cfDNA for Diagnosis and Characterization of CNS Tumors

“…Physiologic factors include those that limit the amount of tumorderived cfDNA present in the CSF. Multiple studies have shown that low grade tumors or those not directly communicating with the CSF space have low to undetectable tumor-derived cfDNA in the CSF Juratli et al, 2018;Martínez-Ricarte et al, 2018;Pan et al, 2019). Likewise, detection of tumor-derived cfDNA is less likely in patients with new onset disease (Pan et al, 2019).…”

“…A panel of seven genes (IDH1, IDH2, TP53, TERT, ATRX, H3F3A, and HIST1H3B) has been developed that can accurately classify nearly 80% of malignant gliomas based on genetics alone. A retrospective study of 20 glioma patients demonstrated that this combined digital PCR and targeted sequencing panel could use CSF cfDNA to correctly classify gliomas in 85% of cases and only failed with low grade tumors or those not in direct contact with the ventricles(Martínez-Ricarte et al, 2018).…”

Review: Peering through a keyhole: liquid biopsy in primary and metastatic central nervous system tumours

“…Regarding the diagnostic potential of CSF cfDNA analysis, evaluation of a selected panel of molecular alterations in CSF cfDNA allowed the identification of tumour molecular alterations in 17/20 (85%) cases of diffuse gliomas, allowing their classification according to the latest WHO criteria . Also, detection of mutations affecting histone H3 genes in a case series of paediatric brain tumours showed high sensitivity and specificity: 87.5% and 100% respectively .…”

Assessment of circulating tumor DNA in pediatric solid tumors: The promise of liquid biopsies

“…In CNS tumors, detection of ctDNA in the peripheral blood is possible, but sensitivity appears to be a challenge in these patients . Instead, recent efforts have focused on detection of tumor DNA in the CSF . Given the paucity of data from studies of ctDNA in children with hematologic and CNS malignancies, our review will focus on current technologies being applied to interrogate ctDNA in children with non‐CNS solid tumors.…”