scholarly journals DIPG-08. ELECTRONIC SEQUENCING PROVIDES OPTIMIZED QUANTIFICATION OF SERIAL, MULTI-GENE MOLECULAR RESPONSE IN THE CSF OF CHILDREN WITH HIGH-GRADE GLIOMA

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii288-iii288
Author(s):  
Amy Bruzek ◽  
Ashwath Muruganand ◽  
Karthik Ravi ◽  
Jack Wadden ◽  
Clarissa Babila ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Limit Of Detection ◽  
High Grade Glioma ◽  
Patient Specific ◽  
Molecular Response ◽  
High Grade ◽  
Non Invasive ◽  
Oxford Nanopore ◽  
Recurrent Mutations ◽  
Analysis Platform

Abstract BACKGROUND For pediatric high-grade glioma (pHGG), non-invasive methods for diagnosis and surveillance are needed. Tumors release DNA (tDNA) into cerebrospinal fluid (CSF), allowing for detection of tumor-associated mutations by CSF sampling. We hypothesized that direct, electronic analysis of tDNA with a novel, hand-held platform (Oxford Nanopore MinION) could quantify patient-specific CSF tDNA variant allele fraction (VAF) with improved speed and limit of detection compared to established methods. METHODS We integrated required multi-timepoint (0, 2, and 6 months) correlate lumbar punctures (LP) in two ongoing pHGG clinical trials. Using Nanopore technology, we performed amplicon-based PCR on CSF tDNA for recurrent mutations from patient samples (n=19) and normal controls. VAF were determined via MinKNOW, Guppy, MiniMap2, and Integrated Genome Browser. RESULTS Nanopore CSF tDNA demonstrated improved sensitivity (91%) when compare to NGS sequencing (50%). Nanopore analysis of serially diluted CSF sample demonstrated significantly lower limit of detection (attomolar) than typical NGS sample requirement (nanomolar). H3K27M mutation was reliably detected with 1,000x depth sequencing, which was achieved in less than 15 minutes of sequencing after amplification. Multiplexed Nanopore analysis of H3F3A and HIST1H3B was employed when H3 status was unknown. Serial CSF tDNA analysis confirmed multi-gene (H3F3A K27M, PIK3CA, and TP53) molecular remission in a 17-year-old with thalamic diffuse midline glioma that correlated with sustained clinical response to ONC201 (14 months and ongoing). CONCLUSIONS Use of a hand-held, electronic DNA analysis platform allows quantification of multi-gene molecular response with improved speed and limit of detection in the CSF of children with high-grade glioma.

scholarly journals PDTM-10. USE OF A NOVEL, HAND-HELD, ELECTRONIC DNA ANALYSIS PLATFORM TO QUANTIFY MULTI-GENE MOLECULAR RESPONSE IN CSF OF PATIENTS WITH HIGH-GRADE GLIOMA

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi188-vi189
Author(s):  
Amy Bruzek ◽  
Leo Tunkle ◽  
Clarissa Babila ◽  
Ashwath Muruganand ◽  
Stefanie Stallard ◽  
...  
Keyword(s):  
Dna Analysis ◽  
High Grade Glioma ◽  
Neurological Injury ◽  
Patient Specific ◽  
P Value ◽  
Molecular Response ◽  
High Grade ◽  
Surgical Biopsy ◽  
Recurrent Mutations ◽  
Droplet Pcr

Abstract BACKGROUND For midline tumors, surgical biopsy risks neurological injury. Non-invasive methods for diagnosis and surveillance are greatly needed. Tumors release DNA into cerebrospinal fluid (CSF-ctDNA), allowing for potential detection and serial monitoring of tumor-associated genetic mutations by CSF sampling. Current detection platforms are limited by their requirement for assay development for each mutation (digital droplet PCR), or cost and timeliness (Illumina sequencing). We hypothesized that direct, electronic analysis of CSF-ctDNA with a novel, hand-held platform (Oxford Nanopore MinION) could provide real-time, ultra-deep sequencing of patient-specific alterations in CSF-ctDNA. METHODS We established multiple clinical trials for pediatric high-grade glioma with required multi-time point (0, 2, and 6 month) correlate lumbar puncture (LP) at time of MRI, with accrual ongoing. We performed amplicon-based PCR on CSF-ctDNA for recurrent mutations and sequenced patient samples (tumor tissue n=8, tumor CSF n=60) and normal controls (tissue n=5, CSF n=24) using NanoPore technology. Variant allele fractions (VAF) were determined via MinKNOW, Guppy, MiniMap2, and Integrated Genome Browser. RESULTS Sensitivity was 79% and specificity 100% by NanoPore. Time from LP to results was 12 hours. A 17-year-old female presented with a biopsy-proven grade IV thalamic glioma with clonal mutations in H3F3A K27M, PIK3CA E545G, TP53 R158G, and TP53 R248Q. After failing standard treatment, she was enrolled in the ONC201 clinical trial and underwent serial LPs. MRI showed stable tumor at 2 months and 40% decrease at 6 months of treatment. H3K27M VAF increased from baseline at 2 months, but decreased to 1% at 6 months of treatment, results that were confirmed by ddPCR. PIK3CA E545G, TP53 R158G, and TP53 R248Q demonstrated the same decrease in VAF, with p-value of < 0.0001. CONCLUSIONS We demonstrate a rapid, reliable method to detect tumor mutations in CSF, and further show molecular remission of H3K27M glioma by CSF sampling.

scholarly journals Electronic DNA Analysis of CSF Cell-free Tumor DNA to Quantify Multi-gene Molecular Response in Pediatric High-grade Glioma

2020 ◽  
Vol 26 (23) ◽  
pp. 6266-6276
Author(s):  
Amy K. Bruzek ◽  
Karthik Ravi ◽  
Ashwath Muruganand ◽  
Jack Wadden ◽  
Clarissa May Babila ◽  
...  
Keyword(s):  
Dna Analysis ◽  
High Grade Glioma ◽  
Molecular Response ◽  
High Grade ◽  
Tumor Dna ◽  
Pediatric High Grade Glioma

scholarly journals OS12.2 Targeting epigenetic pathways in the treatment of recurrent high-grade glioma

2019 ◽  
Vol 21 (Supplement_3) ◽  
pp. iii22-iii22
Author(s):  
A Hau ◽  
L Houben ◽  
E Klein ◽  
A Oudin ◽  
D Stieber ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Drug Response ◽  
High Grade Glioma ◽  
Differential Sensitivity ◽  
Targeted Sequencing ◽  
Patient Specific ◽  
Comparative Genomic ◽  
High Grade ◽  
Evolutionary Trajectory ◽  
Tumor Organoids

Abstract BACKGROUND High grade glioma (HGG) patients develop resistance to standard treatment leading to disease progression and limited life expectancy. Advances in the molecular characterisation of treatment-naïve HGGs based on next-generation sequencing and DNA methylation analyses have led to a better delineation of HGG subtypes and the identification of distinct genomic abnormalities. Furthermore, using large patient cohorts of longitudinal tumor samples, comprehensive genomic profiling studies emerged to investigate therapy-associated evolution of gliomas. All together, those studies point out the need for personalised treatment strategies, where applied drugs will be adapted to the unique patient-specific genetic abnormalities. MATERIAL AND METHODS We collected fresh samples of more than 800 brain tumors containing almost 300 glioma specimen with approximately 100 longitudinal samples of initial and recurrent tumors from 43 matched patients. By now, we have successfully established 34 patient-derived orthotopic xenografts (PDOXs) in mice. We performed comprehensive molecular profiling using array comparative genomic hybridisation, DNA methylation analysis and targeted DNA sequencing on patient specimen and their derivatives such as 3D tumor organoids and PDOXs. The custom-design sequencing panel comprises 234 genes that reflect both established genetic identifiers for individual glioma subtype classification and novel genes encoding mainly epigenetic effector genes. Based on patient-derived material we carried out drug response screening on 3D tumor organoids using a compound library matching the majority of genes that were assessed by targeted sequencing. RESULTS We succeeded in generating a live biobank of HGG patient-derived xenografts and 3D organoids that neatly recapitulates the mutational spectrum including structural DNA variation and methylation-based subtypes of gliomas. A highlight is the generation of 19 PDOXs of paired initial and relapse HGGs from a total of 9 glioma patients. A detailed analysis of the paired longitudinal samples indicated that PDOX models closely recapitulate the evolutionary trajectory of the parental tumors. Targeted sequencing of longitudinal HGG PDOXs suggests that relapse tumors accumulate somatic mutations in epigenetic effectors compared with the Initial. Differential drug responses between initial and relapse tumors were observed after screening of in vitro 3D tumor organoids. CONCLUSION Response assessment of naïve initial gliomas and recurrences provides crucial information on the differential sensitivity between initial and relapsed HGGs and offers novel personalised therapeutic options in the relapse setting. Furthermore, in depth correlation of the profiled somatic molecular landscape with drug response will enable pharmacogenomic predictions of potential inhibitors in the clinical setting.

scholarly journals Individual Patient-Specific Immunity against High-Grade Glioma after Vaccination with Autologous Tumor Derived Peptides Bound to the 96 KD Chaperone Protein

2012 ◽  
Vol 19 (1) ◽  
pp. 205-214 ◽  
Author(s):  
Courtney A. Crane ◽  
Seunggu J. Han ◽  
Brian Ahn ◽  
Jessica Oehlke ◽  
Valerie Kivett ◽  
...  
Keyword(s):  
High Grade Glioma ◽  
Patient Specific ◽  
Autologous Tumor ◽  
High Grade ◽  
Specific Immunity ◽  
Chaperone Protein

scholarly journals INNV-16. CLINICAL APPLICABILITY OF INDIVIDUALIZED DRUG RESPONSE PROFILING UTILIZING EX-VIVO TISSUE-DERIVED 3D CELL CULTURE ASSAYS IN HIGH-GRADE GLIOMA: A SINGLE INSTITUTION CASE SERIES USING 3D-PREDICT RESULTS

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii119-ii120
Author(s):  
Lindsay Lipinski ◽  
Ajay Abad ◽  
Laszlo Mechtler ◽  
Andrew Fabiano ◽  
Ashley Smith ◽  
...  
Keyword(s):  
Cell Culture ◽  
Drug Response ◽  
Ex Vivo ◽  
Performance Status ◽  
Case Series ◽  
3D Cell Culture ◽  
High Grade Glioma ◽  
Patient Specific ◽  
High Grade ◽  
Ex Vivo Tissue

Abstract Recurrent high-grade glioma is a challenging disease process, without consensus on effective second-line therapy options. Individualized, patient-specific, biologically-based data is desirable in driving therapeutic decision-making. Patients with recurrent high-grade glioma and planned surgical re-resection at our institution were prospectively enrolled into the 3D-PREDICT study. Tissue was collected at the time of surgery for ex vivo 3D cell culture assays comprising a panel of agents commonly used for high-grade glioma, including chemotherapies and targeted therapies used in other solid cancers. In all cases, therapeutic agent selection was guided by the neuro-oncologist’s clinical judgement, factoring the patient’s age, performance status, comorbidities, toxicities/side effect profile of potential agents, and drug accessibility, plus ex-vivo drug response RESULTS: We present 3 cases in which the selection of agents was influenced by the tissue-derived 3D cell culture results; treatment led to clinical response observed in terms of progression free survival, quality of life, and pharmacologic tolerability. In Case 1, a patient with recurrent anaplastic astrocytoma was treated with a BRAF inhibitor for 12 months with excellent tolerability and no radiographic progression. Case 2 demonstrates the use of combination bevacizumab and irinotecan after disease progression subsequent to standard treatment. This patient had local radiographic control for 7 months, tolerating the regimen well. In Case 3, an individual with recurrent glioblastoma was treated with combination carboplatin and etoposide based on assay response prediction to both agents; treatment has been tolerated well with radiographic stability at 6 months while maintaining good performance status. This case series represents our institutional experience of utilizing patient-specific, ex-vivo tissue-derived cell drug response profiling to guide choice of therapy for recurrent high-grade glioma patients. Using individualized, tumor-specific drug sensitivity data to guide these decisions is representative of the ongoing paradigm shift into the realm of individualized medicine to improve outcomes in cancer patients.

scholarly journals Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer

2019 ◽  
Vol 11 (504) ◽  
pp. eaax7392 ◽  
Author(s):  
Bradon R. McDonald ◽  
Tania Contente-Cuomo ◽  
Stephen-John Sammut ◽  
Ahuva Odenheimer-Bergman ◽  
Brenda Ernst ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Neoadjuvant Therapy ◽  
Dna Analysis ◽  
Residual Disease ◽  
Circulating Tumor Dna ◽  
Patient Specific ◽  
Molecular Response ◽  
Curative Intent ◽  
Current Limit ◽  
Tumor Dna

Longitudinal analysis of circulating tumor DNA (ctDNA) has shown promise for monitoring treatment response. However, most current methods lack adequate sensitivity for residual disease detection during or after completion of treatment in patients with nonmetastatic cancer. To address this gap and to improve sensitivity for minute quantities of residual tumor DNA in plasma, we have developed targeted digital sequencing (TARDIS) for multiplexed analysis of patient-specific cancer mutations. In reference samples, by simultaneously analyzing 8 to 16 known mutations, TARDIS achieved 91 and 53% sensitivity at mutant allele fractions (AFs) of 3 in 104 and 3 in 105, respectively, with 96% specificity, using input DNA equivalent to a single tube of blood. We successfully analyzed up to 115 mutations per patient in 80 plasma samples from 33 women with stage I to III breast cancer. Before treatment, TARDIS detected ctDNA in all patients with 0.11% median AF. After completion of neoadjuvant therapy, ctDNA concentrations were lower in patients who achieved pathological complete response (pathCR) compared to patients with residual disease (median AFs, 0.003 and 0.017%, respectively, P = 0.0057, AUC = 0.83). In addition, patients with pathCR showed a larger decrease in ctDNA concentrations during neoadjuvant therapy. These results demonstrate high accuracy for assessment of molecular response and residual disease during neoadjuvant therapy using ctDNA analysis. TARDIS has achieved up to 100-fold improvement beyond the current limit of ctDNA detection using clinically relevant blood volumes, demonstrating that personalized ctDNA tracking could enable individualized clinical management of patients with cancer treated with curative intent.

scholarly journals Image-based personalization of computational models for predicting response of high-grade glioma to chemoradiation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
David A. Hormuth ◽  
Karine A. Al Feghali ◽  
Andrew M. Elliott ◽  
Thomas E. Yankeelov ◽  
Caroline Chung
Keyword(s):  
Mathematical Models ◽  
Computational Models ◽  
Tumor Response ◽  
Treatment Resistance ◽  
High Grade Glioma ◽  
Information Criteria ◽  
Patient Specific ◽  
Model Parameters ◽  
High Grade ◽  
High Grade Gliomas

AbstractHigh-grade gliomas are an aggressive and invasive malignancy which are susceptible to treatment resistance due to heterogeneity in intratumoral properties such as cell proliferation and density and perfusion. Non-invasive imaging approaches can measure these properties, which can then be used to calibrate patient-specific mathematical models of tumor growth and response. We employed multiparametric magnetic resonance imaging (MRI) to identify tumor extent (via contrast-enhanced T1-weighted, and T2-FLAIR) and capture intratumoral heterogeneity in cell density (via diffusion-weighted imaging) to calibrate a family of mathematical models of chemoradiation response in nine patients with unresected or partially resected disease. The calibrated model parameters were used to forecast spatially-mapped individual tumor response at future imaging visits. We then employed the Akaike information criteria to select the most parsimonious member from the family, a novel two-species model describing the enhancing and non-enhancing components of the tumor. Using this model, we achieved low error in predictions of the enhancing volume (median: − 2.5%, interquartile range: 10.0%) and a strong correlation in total cell count (Kendall correlation coefficient 0.79) at 3-months post-treatment. These preliminary results demonstrate the plausibility of using multiparametric MRI data to inform spatially-informative, biologically-based predictive models of tumor response in the setting of clinical high-grade gliomas.

scholarly journals Intermittent radiotherapy as alternative treatment for recurrent high grade glioma: a modeling study based on longitudinal tumor measurements

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sarah C. Brüningk ◽  
Jeffrey Peacock ◽  
Christopher J. Whelan ◽  
Renee Brady-Nicholls ◽  
Hsiang-Hsuan M. Yu ◽  
...  
Keyword(s):  
Tumor Growth ◽  
Treatment Option ◽  
Radiation Treatment ◽  
Phase 1 ◽  
High Grade Glioma ◽  
Patient Specific ◽  
Tumor Control ◽  
Model Parameters ◽  
High Dose ◽  
High Grade

AbstractRecurrent high grade glioma patients face a poor prognosis for which no curative treatment option currently exists. In contrast to prescribing high dose hypofractionated stereotactic radiotherapy (HFSRT, $$\ge 6$$ ≥ 6 Gy $$\times$$ × 5 in daily fractions) with debulking intent, we suggest a personalized treatment strategy to improve tumor control by delivering high dose intermittent radiation treatment (iRT, $$\ge 6$$ ≥ 6 Gy $$\times$$ × 1 every 6 weeks). We performed a simulation analysis to compare HFSRT, iRT and iRT plus boost ($$\ge 6$$ ≥ 6 Gy $$\times$$ × 3 in daily fractions at time of progression) based on a mathematical model of tumor growth, radiation response and patient-specific evolution of resistance to additional treatments (pembrolizumab and bevacizumab). Model parameters were fitted from tumor growth curves of 16 patients enrolled in the phase 1 NCT02313272 trial that combined HFSRT with bevacizumab and pembrolizumab. Then, iRT +/− boost treatments were simulated and compared to HFSRT based on time to tumor regrowth. The modeling results demonstrated that iRT + boost(− boost) treatment was equal or superior to HFSRT in 15(11) out of 16 cases and that patients that remained responsive to pembrolizumab and bevacizumab would benefit most from iRT. Time to progression could be prolonged through the application of additional, intermittently delivered fractions. iRT hence provides a promising treatment option for recurrent high grade glioma patients for prospective clinical evaluation.

scholarly journals iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone

2020 ◽  
Author(s):  
Aspyn Palatnick ◽  
Bin Zhou ◽  
Elodie Ghedin ◽  
Michael C. Schatz
Keyword(s):  
High Performance ◽  
Dna Analysis ◽  
Computer Hardware ◽  
Nanopore Sequencing ◽  
Mobile Dna ◽  
Mobile Environment ◽  
Sequencing Platform ◽  
Link Type ◽  
Oxford Nanopore ◽  
Analysis Platform

AbstractFollowing the miniaturization of integrated circuitry and other computer hardware over the past several decades, DNA sequencing is following a similar path. Leading this trend is the Oxford Nanopore sequencing platform, which currently offers the hand-held MinION instrument and even smaller instruments on the near horizon. This technology has been used in several important applications, including the analysis of genomes of major pathogens in remote stations around the world. However, despite the simplicity of the sequencer, an equally simple and portable analysis platform is not yet available.iGenomics is the first comprehensive mobile genome analysis application, with capabilities to align reads, call variants, and visualize the results entirely on an iOS device. Implemented in Objective-C using the FM-index, banded dynamic programming, and other high-performance bioinformatics techniques, iGenomics is optimized to run in a mobile environment. We benchmark iGenomics using a variety of real and simulated Nanopore sequencing datasets and show that iGenomics has performance comparable to the popular BWA-MEM/Samtools/IGV suite, without needing a laptop or server cluster. iGenomics is available open-source (https://github.com/stuckinaboot/iGenomics) and for free on Apple’s App Store (https://apps.apple.com/us/app/igenomics-mobile-dna-analysis/id1495719841).

scholarly journals 18F-FAZA PET imaging in tumor hypoxia: A focus on high-grade glioma

2020 ◽  
Vol 35 (1_suppl) ◽  
pp. 42-46 ◽  
Author(s):  
Paola Mapelli ◽  
Maria Picchio
Keyword(s):  
Tumor Hypoxia ◽  
High Grade Glioma ◽  
Short Review ◽  
Typical Feature ◽  
Emission Tomography ◽  
High Grade ◽  
Malignant Cells ◽  
Hostile Environment ◽  
Non Invasive ◽  
Positron Emission

The presence of hypoxia is a typical feature of solid tumors and has been identified in many neoplasms, favouring the survival of malignant cells in a hostile environment and the expression of an aggressive phenotype. Malignant brain tumors have large proportions of hypoxic tissue, thus contributing to resistance to radiation and chemotherapy. Positron emission tomography (PET) is an attractive technique to gain a non-invasive assessment of tumor hypoxia within the whole tumor, with 18F-fluoromisonidazole (18F-FMISO) and 18F-flouroazomycin arabinoside (18F-FAZA) being the most promising radiotracers. In this short review, we aim to discuss the available clinical studies focused on the use of 18F-FAZA PET/computed tomography in patients affected by high-grade glioma.

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