Abstract A09: Cerebrospinal fluid (CSF) as a source of ctDNA for diagnosis and monitoring of pediatric patients with midline diffuse gliomas
Bibliographic record
Abstract
Abstract Background: Midline diffuse gliomas are aggressive pediatric tumors, characterized molecularly by the presence of H3K27 mutation. These tumors are extremely malignant, with median overall survival of less than a year. Localized mainly in the pons or thalamic regions, they are not amenable to a gross total resection; however, a biopsy is needed for pathologic and molecular diagnosis. In this scenario, liquid biopsy is of utmost importance and has the potential to spare the risk of morbidity with surgical procedures, determine diagnosis and prognosis, as well as serve as a tool to identify potential targetable alterations. The objective of this pilot feasibility study is to explore the use of CSF ctDNA using ddPCR and next-generation sequencing tools to diagnose and monitor patients with midline diffuse gliomas. Methods: We extracted CSF ct DNA collected from external ventricular drain in two patients diagnosed with midline diffuse glioma (one thalamic glioblastoma, one DIPG). ctDNA was extracted from 2 mL of CSF, quantification was done by quibit, and samples were processed first with ddPCR for detection of H3K27M point mutation followed by comprehensive profiling by whole-exome sequencing using Illumina HiSeq2500 sequencer. We assessed the feasibility of identifying diagnostic point mutations, as well as potential evolution of the tumor molecular landscape at disease progression. Results: The first case, a thalamic GBM, had tissue available for molecular analysis; targeted RNA sequencing was performed on a clinical basis detecting H3K27M mutation (VAF=43%) and a PDGFRA N659K mutation (VAF=43%). ddPCR analysis of the CSF ctDNA identified the H3K27M mutation with VAF of 14%. Whole-exome sequencing (WES) confirmed the presence of H3K27M point mutation at VAF 11% and PDGFRA mutation at VAF 13%. This patient received radiation and chemotherapy but progressed rapidly and passed 7 months after the diagnosis. The second case, a DIPG diagnosed upon radiologicl and clinical criteria, was previously treated with conventional focal radiation and needed an EVD upon massive leptomeningeal progression with associated meningitis. CSF was then processed for ctDNA analysis. ddPCR confirmed the presence of H3K27M mutation with VAF of 48%. WES confirmed the presence of H3K27M mutation (VAF 14%) and additional TP53 R273C point mutation with VAF of 87%. This patient passed roughly 11 months post diagnosis. Conclusion: We have demonstrated the feasibility of detection of molecular markers in CSF through ddPCR and NGS platform to not only to assist in diagnosis of pediatric midline diffuse gliomas, but also to monitor these patients for additional/new molecular events that may be targetable. Building on these results, we are currently implementing a targeted sequencing panel to establish the specificity of this method in a large pediatric brain tumor cohort. Citation Format: Liana Nobre, Robert Siddaway, Monique Johnson, Scott Ryall, Michal Zapotocky, Julie Bennet, Uri Tabori, Cynthia Hawkins. Cerebrospinal fluid (CSF) as a source of ctDNA for diagnosis and monitoring of pediatric patients with midline diffuse gliomas [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A09.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".