MBRS-20. CSF-DERIVED CIRCULATING TUMOR DNA AS A BIOMARKER FOR DISEASE PROGRESSION AND TUMOR EVOLUTION IN MEDULLOBLASTOMA

Abstract BACKGROUND Cell-free DNA (cfDNA) profiling has been shown to carry utility as a clinically relevant biomarker in a variety of cancers, but studies in pediatric brain tumors, including medulloblastoma, are scarce. We hereby evaluated the actionability of profiling cfDNA from cerebrospinal fluid (CSF) based on a multi-institutional cohort of children with medulloblastoma. METHODS 103 children aged ≥ 3 years with medulloblastoma harboring chromosomal aneuploidy enrolled on two prospective therapeutic trials were included. cfDNA was extracted from CSF obtained longitudinally, and profiled by low-coverage whole-genome sequencing (lcWGS) for annotating copy-number variants (CNVs). cfDNA-derived CNVs were compared against patient-matched primary tumor-derived CNVs and correlated with outcome. cfDNA profiles at diagnosis and relapse were compared to evaluate tumor evolution. RESULTS Tumor-derived somatic CNVs were detected in 72% of baseline cfDNA samples, with higher detection rate in samples from patients with metastatic disease than those without (90% versus 50%, chi-square p=0.001). Longitudinal profiling of cfDNA revealed correlation between CNV detectability and clinical course, with detection of tumor-derived CNVs in cfDNA samples predating radiographic progression for ≥ 3 months in 62% of relapsing patients. Presence of cfDNA-derived CNVs in CSF collected during chemotherapy and at the end of therapy was significantly associated with inferior PFS (log-rank p<0.0001 for both time-points). Comparison of CNV profiles from cfDNA at baseline and relapse revealed molecular divergence in a subset of patients. CONCLUSION These results carry major implications and supports the incorporation of cfDNA profiling in upcoming medulloblastoma protocols for more sensitive and accurate disease monitoring and personalization of treatment.

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PATH-18. CSF-DERIVED CIRCULATING TUMOR DNA REFLECTS DISEASE COURSE AND CLONAL EVOLUTION IN MEDULLOBLASTOMA

Neuro-Oncology ◽

10.1093/neuonc/noz175.614 ◽

2019 ◽

Vol 21 (Supplement_6) ◽

pp. vi146-vi147

Author(s):

Anthony P Y Liu ◽

Rahul Kumar ◽

Kyle Smith ◽

Giles Robinson ◽

Amar Gajjar ◽

...

Keyword(s):

Clonal Evolution ◽

Disease Status ◽

Pediatric Brain Tumors ◽

Circulating Tumor Dna ◽

Tumor Evolution ◽

Longitudinal Assessment ◽

Primary Tumors ◽

Suboptimal Outcome ◽

Dismal Prognosis ◽

Tumor Dna

Abstract Medulloblastoma (MB) is the most common malignant brain tumor in young children. A multi-modal approach comprises standard of care, and recent advances in molecular studies have identified clinically relevant subgroups. Nonetheless, 30% of MB patients relapse or progress, conferring dismal prognosis. Such suboptimal outcome is partly due to a lack of sensitive biomarkers for response-adapted personalization of treatment and relapse prediction. Circulating tumor DNA has been shown to correlate with disease status in a variety of adult cancers, but studies in pediatric brain tumors, including medulloblastoma, are scarce. Here, we aim to evaluate the utility of profiling cell-free DNA (cfDNA) derived from longitudinally-banked cerebrospinal fluid (CSF) samples collected from children with MB enrolled in two prospective, multi-center trials (SJMB03 and SJMB12, estimated sample size of 100 patients, including 50 with subsequent progression). cfDNA was extracted, quantified, and analyzed for size distribution from pre-centrifuged CSF serially banked during the course of treatment and follow-up. Low-pass whole genome sequencing (LP-WGS) enabled detection of chromosomal and focal copy number alterations (CNAs). CNAs detected in cfDNA were compared against known somatic changes in corresponding primary tumors. Detectability of tumor-specific CNAs in cfDNA was then correlated with tumor burden and patient outcome. Pilot analysis showed presence of arm level and/or focal CNAs in cfDNA from 80% of CSF samples in 20 children with metastatic MB, and longitudinal assessment revealed correlation with clinical course throughout treatment with radiotherapy and chemotherapy. Further comparison of tumor and longitudinal cfDNA derived CNAs revealed divergent genomic alterations implicating potential oncogenic mechanisms underlying treatment failure and recurrence. Our study performed on a large prospective series of MB trial patients substantiates the utility of CSF derived cfDNA as an actionable biomarker in high-risk MB patients while also facilitating understanding of tumor evolution and heterogeneity.

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Pediatric Brain tumors in Southeast Nigeria; An 8-year prospective longitudinal cohort study

10.21203/rs.2.13963/v1 ◽

2019 ◽

Author(s):

Enoch Uche ◽

Nkechi Judith Uche ◽

Obinna V Ajuzieogu ◽

Dubem Amuta ◽

ephraim Onyia ◽

...

Keyword(s):

Brain Tumors ◽

Survival Rates ◽

Pediatric Brain Tumors ◽

Common Symptom ◽

Chi Square ◽

Study Results ◽

Chi Square Test ◽

Poor Outcomes ◽

Prospective Longitudinal ◽

Pediatric Brain

Abstract Background: Pediatric brain tumors (PBT’s) from previous studies are associated with poor outcomes in our subregion. Methods. An 8 -year single center prospective study. All cases investigated with neuroimaging and treated were enrolled. Data was analyzed with SPSS (Inc) Chicago IL, USA version 23. Chi Square test, One-way Anova and confidence limits were used to evaluate associations using the 95% level of significance. Patients were followed up for a range of 1 to 7.5 years with a mean of 4.9 ±1.3years. Ethical approval was obtained for our study. Results: 95 patients were enrolled, 84 satisfied the study criteria. There were 45 males and 39 females, M: F=1.1. The mean age was 9.9±2.7 years 95%CI with a range of 9 months to 16 years. The most common symptom was headache for supratentorial lesions (73%) and gait disturbance (80.2%) for infratentorial lesions. More tumors were supratentorial in location (45(54.2%), while 33(37.1%) were infratentorial. Craniopharyngiomas (n=19), medulloblastomas(n=17) and astrocytomas (n=11) were the most common tumors. Hemoglobin genotype(AA and AS) had some influence on tumor phenotype, Odds ratio 8.9 and 3.3 for medulloblastoma and craniopharyngioma. 69 cases were microsurgically resected while 14 patients were treated with radiotherapy alone. The 30-day mortality for operated cases is 7.9±1.3%. Overall 1-year and 5-year survival was 67.9% and 53.6 % respectively. Survival rates varied among treatment groups (X2=8.9, P=0.017). Conclusion: Survival profile in this series suggests some improvement in comparison to previous studies from our region.

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Pediatric Brain tumors in Southeast Nigeria; A prospective longitudinal cohort study

10.21203/rs.2.13963/v2 ◽

2019 ◽

Author(s):

Enoch Uche ◽

Nkechi Judith Uche ◽

Obinna V Ajuzieogu ◽

Dubem Amuta ◽

ephraim Onyia ◽

...

Keyword(s):

Brain Tumors ◽

Pediatric Brain Tumors ◽

Common Symptom ◽

Chi Square ◽

Study Results ◽

Ethical Approval ◽

Chi Square Test ◽

Poor Outcomes ◽

Prospective Longitudinal ◽

Pediatric Brain

Abstract Background: Pediatric brain tumors (PBT’s) from previous studies are associated with poor outcomes in our sub region. Methods. An 8 -year single center prospective study. All cases investigated with neuroimaging and treated were enrolled. Data was analyzed with SPSS (Inc.) Chicago IL, USA version 23. Chi Square test, One-way Anova and confidence limits were used to evaluate associations at the 95% level of significance. Ethical approval was obtained for our study. Results: 103 patients were enrolled, 92 satisfied the study criteria. There were 45 males and 39 females, M: F=0.8. The mean age was 9.5±2.1 years 95%CI with a range of 7 months to 16 years. The most common symptom was headache for supratentorial lesions (73%) and gait disturbance (80.2%) for infratentorial lesions. More tumors were supratentorial in location (51 (55.4%), while 35(38.1%) were infratentorial. Craniopharyngiomas (n=22), medulloblastomas (n=17) and astrocytomas (n=12) were the most common tumors. Hemoglobin genotype (AA and AS) had some influence on tumor phenotype FT, P=0.033. 76 cases were microsurgically resected while 16 patients were treated with radiotherapy alone. The 30-day mortality for operated cases is 7.2±0.7%. Overall 1-year and 5-year survival was 66.7% and 52.3 % respectively. Survival School performance varied among treatment subgroups Conclusion: Survival profile in this series suggests some improvement in comparison to previous studies from our region. Keywords: Pediatric brain tumors, microneurosurgery, radiotherapy, survival

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Quantifying the evolution of tumor architecture using serial circulating tumor DNA.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.4_suppl.600 ◽

2019 ◽

Vol 37 (4_suppl) ◽

pp. 600-600

Author(s):

Jason Henry ◽

Jonathan M. Loree ◽

John H. Strickler ◽

Kanwal Pratap Singh Raghav ◽

Van K. Morris ◽

...

Keyword(s):

Allele Frequency ◽

Limit Of Detection ◽

Circulating Tumor Dna ◽

Tumor Evolution ◽

Disease Course ◽

Serial Sampling ◽

Blood Specimens ◽

Serial Samples ◽

Tumor Dna ◽

Over Time

600 Background: There is limited data regarding changes in the genomic landscape in individual patients over time as serial tissue biopsy has risk and is of uncertain clinical benefit. The advent of circulating tumor DNA (ctDNA) allows for safe and repeated molecular sampling with the potential to investigate evolution of tumor architecture over the disease course. Methods: From 5/15 to 12/17, 116 patients with metastatic CRC had between three to 12 blood specimens taken over the treatment course. Plasma was tested using targeted NGS assay (Guardant360, Guardant Health, 68 gene). To account for variations in the amount of ctDNA in serial samples, a window of evaluable allele frequency was established for each patient as the fold change between the max allele frequency (mAF) and limit of detection for serial samples with the lowest mAF. Mutations not falling within this window were excluded from analysis. Substantial treatment induced selective pressure (SP) was defined as a decrease in the mutant mAF of > 50% in patients with at least an initial mAF of 1%. Results: 116 patients with a total of 317 serial blood samples were evaluable after accounting for ctDNA variations over time. Specimens were collected a median of 12 months apart, with a median of three specimens per patient. Thirteen patients (11%) did not have any changes in mutations on serial sampling, however the remainder of patients gained an average of 1.1 mutations per time point (mut/tp), and lost 1.0 mut/tp. 31% of patients demonstrated evidence of substantial treatment-induced SP. These patients were more likely to demonstrate a change in clonal architecture of the tumor (46% greater rate than those without SP, P = 0.04), predominantly through gain of new clones. In contrast, clonal hematopoiesis alterations that may be induced by chemotherapy, such as JAK2V617F, were neither gained or lost. Conclusions: After correction for variations over time in the total amount of ctDNA in circulation, we identify numerous changes in tumor architecture with serial sampling. For the first time in colorectal cancer we demonstrate that when treatment-induced SP is applied the rate of tumor evolution is increased, demonstrating potential value of monitoring changes in tumor architecture over the disease course.

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Circulating tumor DNA (ctDNA) landscape in metastatic castrate-resistant prostate cancer patients with germline alterations.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.6_suppl.200 ◽

2020 ◽

Vol 38 (6_suppl) ◽

pp. 200-200

Author(s):

Marcus W. Moses ◽

Peter Steinwald ◽

Ellen Jaeger ◽

Whitley Hatton ◽

Patrick Cotogno ◽

...

Keyword(s):

Prostate Cancer ◽

San Francisco ◽

Splice Variants ◽

Circulating Tumor Dna ◽

P Value ◽

Fisher Exact Test ◽

Chi Square ◽

Exact Test ◽

Viable Approach ◽

Tumor Dna

200 Background: Circulating tumor-DNA (ctDNA) in mCRPC patients (pts) provides a viable approach for examining the genetic landscape of prostate cancer. In this follow-up, we report ctDNA variants in germline tested mCRPC pts. Methods: ctDNA alterations in 73 genes were detected using Guardant360 (G360) assays. Alteration types assessed were missense, frameshift, insertions, splice variants, truncations, amplifications (amp), deletions, and other. Pts included in the analysis received germline genetic testing (Invitae Corporation, San Francisco, CA) and ctDNA assays at various treatment timepoints. Statistical analyses were performed using chi-square and fisher exact test with p-value <0.05 for significance. Results: Germline and ctDNA testing was completed in 270 mCRPC pts. 13% (35/270) of pts had pathogenic germline alterations. Germline alterations detected were BRCA2 (43%, n=15), ATM (8.5%, n=3), CHEK2 (8.5%, n=3), and BRCA1 (6%, n=2). Of the 673 alterations detected in G360 assays, TP53 (25%, n=167) and AR (17%, n=117) were most commonly observed. ctDNA alteration breakdown for germline negative/positive pts is summarized in Tables A/B. Germline negative pts had more AR alterations compared to germline positive (p = 0.023). Also, germline negative pts presented with more amps (p < 0.001) and germline positive pts with more frameshift alterations (p = 0.005). The association of ctDNA alteration to clinical outcomes in germline positive/negative pts was also assessed and is ongoing. Conclusions: Pts with germline positive alterations had few somatic AR alterations and higher frequency of deleterious mutation in comparison to their germline negative counterparts.[Table: see text][Table: see text]

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Non-invasive diagnosis and tracking of tumor evolution by targeted sequencing of circulating tumor DNA in metastatic pancreatic cancer patients.

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.e15769 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. e15769-e15769

Author(s):

Thomas Seufferlein ◽

Andreas W. Berger ◽

Daniel Schwerdel ◽

Thomas Jens Ettrich ◽

Stefan A. Schmidt ◽

...

Keyword(s):

Tumor Tissue ◽

Early Stage ◽

Therapy Monitoring ◽

Circulating Tumor Dna ◽

Ductal Adenocarcinoma ◽

Tumor Evolution ◽

Imaging Data ◽

Non Invasive ◽

Outcome Monitoring ◽

Tumor Dna

e15769 Background: Treatment of stage IV pancreatic ductal adenocarcinoma (PDAC) has made substantial progress over the last years, therapy monitoring still is at an early stage. This could be substantially supported by tools that allow to establish and monitor the molecular setup of the tumor even during treatment. In particular, non-invasive approaches are desirable. Characterization of circulating tumor DNA (ctDNA) may help to achieve this goal. Methods: We analyzed a cohort of 20 patients with histologically confirmed metastatic PDAC (mPDAC) prior to and during palliative treatment including disease progression. ctDNA and corresponding tumor tissue were analyzed by targeted NGS and droplet digital PCR for the 7 most frequently mutated genes in PDAC ( TP53, SMAD4, CDKN2A, KRAS, APC, ATM, FBXW7). Findings were correlated with clinical and imaging data to establish its prognostic and predictive value. Results: ctDNA was analyzed at baseline prior to initiation of the respective line of treatment. Mutations in either of the genes examined were detectable in 15/20 patients (75%). Tissue-blood concordance was 80% in therapy naïve patients. 96% of mutations in ctDNA of therapy naïve patients were in KRAS and/or TP53. The combined mutated allele frequencies (CMAF) of theese 2 genes significantly decreased (p = 0.0173) during therapy and increased at progression (p = 0.0145) across all treatment lines. By sequential ctDNA analyses we detected a change in the mutational landscape compared to the respective baseline ctDNA status in 7/11 patients during 1st line, in 3/7 patients during 2nd line and 2/2 patients during 3rdline treatment. In therapy naïve patients, the decline of the CMAF during therapy significantly correlated with progression-free survival (p = 0.0013). Conclusions: Molecular genotyping of ctDNA in mPDAC patients proved to be feasible and there was a high concordance between tumor tissue and ctDNA. The molecular genotype changed significantly during treatment and changes correlated with outcome. Monitoring of ctDNA may enable to adapt therapeutic strategies to the specific molecular changes present at a certain time during treatment of mPDAC.

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Profiling 523 cancer associated genes in circulating tumor DNA of children with CNS tumors.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.3023 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 3023-3023

Author(s):

Erin R. Bonner ◽

Robin Harrington ◽

Biswajit Das ◽

Paul M. Williams ◽

Chris Alan Karlovich ◽

...

Keyword(s):

Liquid Biopsy ◽

Molecular Subtype ◽

Circulating Tumor Dna ◽

Copy Number Variations ◽

Response To Therapy ◽

Cns Tumors ◽

Response To Treatment ◽

Tumor Evolution ◽

Cns Tumor ◽

Tumor Dna

3023 Background: Pediatric central nervous system (CNS) cancers often pose unique challenges including tumor ‘invisibility’, where surgical resection is restricted due to the sensitive tumor location and tissue biopsy is not always feasible. Detecting cancer associated mutations and copy number variations (CNV) at diagnosis is increasingly important, as the WHO classification of pediatric CNS cancers has incorporated molecular signatures with tumor grade. To achieve CNS tumor molecular ‘visibility’, we previously established a liquid biopsy platform for detecting single nucleotide variants in circulating tumor DNA (ctDNA). However, our method was limited by the restricted number of genes that can be monitored and the inability to detect genomic events including CNVs. To address this, we developed a deep sequencing liquid biopsy approach to profile alterations across selected genes. Our platform provides an opportunity for multi-gene monitoring, to assess tumor subclonal evolution and response to treatment in the absence of repeat tissue biopsies. Methods: We tested the performance of our platform using paired tissue, CSF, and plasma/serum from 10 children with diffuse midline glioma (DMG). ctDNA was analyzed using the TruSight Oncology 500 (TSO500) ctDNA targeted panel covering 523 genes. Matched tumor, CSF, and blood were assessed for concordance and sequencing results were compared to digital droplet PCR (ddPCR) detection of H3K27M mutation. Results: The median exons with ³500X coverage was 96% for 7 CSF samples with optimal input (³60ng), 0.01% for 3 CSF samples with < 5ng input, and 74.5% for plasma/serum samples. ctDNA was more readily detectable in CSF, yet concordance between paired tumor, CSF and plasma/serum was observed. DMG associated mutations in genes including H3F3A, HIST1H3B, TP53, and ACVR1 were detected in ctDNA. Of 9 H3K27M mutations identified in tumor, 8 were present in CSF and 3 in plasma/serum, for a positive percent agreement of 89% and 33%, respectively, with the tumor results. Among CSF samples, H3.3K27M was detected in 6/6 cases, and H3.1K27M in 2/3 cases, with variant allele frequencies comparable to ddPCR results. CNVs including PDGFRA/B and MDM4 amplifications were present in CSF and confirmed by analysis of paired tumor. Additional events, including PIK3CA p.E545Q, PPM1D truncation, and KRAS amplification, were detected in CSF but absent from paired tumor, indicating tissue heterogeneity. Strategies to optimize ctDNA detection, including optimization of ctDNA isolation and adjustment of library QC metrics, were identified. Conclusions: This proof-of-concept study demonstrates the feasibility of our high depth, targeted sequencing approach for detecting clinically relevant mutations in ctDNA from children with CNS tumors. This approach may aid in diagnosis of CNS tumor molecular subtype, and monitoring of tumor evolution and response to therapy in serially collected ctDNA.

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A Study of Hypermethylated Circulating Tumor DNA as a Universal Colorectal Cancer Biomarker

Clinical Chemistry ◽

10.1373/clinchem.2015.253609 ◽

2016 ◽

Vol 62 (8) ◽

pp. 1129-1139 ◽

Cited By ~ 67

Author(s):

Sonia Garrigou ◽

Geraldine Perkins ◽

Fanny Garlan ◽

Corinne Normand ◽

Audrey Didelot ◽

...

Keyword(s):

Colorectal Cancer ◽

Genetic Material ◽

Surrogate Marker ◽

Digital Pcr ◽

Tumor Stage ◽

Circulating Tumor Dna ◽

Tumor Evolution ◽

Highly Sensitive ◽

Tumor Dna

Abstract BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a good candidate for tracking tumor dynamics in different cancer types, potentially avoiding repeated tumor biopsies. Many different genes can be mutated within a tumor, complicating procedures for tumor monitoring, even with highly sensitive next-generation sequencing (NGS) strategies. Droplet-based digital PCR (dPCR) is a highly sensitive and quantitative procedure, allowing detection of very low amounts of circulating tumor genetic material, but can be limited in the total number of target loci monitored. METHODS We analyzed hypermethylation of 3 genes, by use of droplet-based dPCR in different stages of colorectal cancer (CRC), to identify universal markers for tumor follow-up. RESULTS Hypermethylation of WIF1 (WNT inhibitory factor 1) and NPY (neuropeptide Y) genes was significantly higher in tumor tissue compared to normal tissue, independently of tumor stage. All tumor tissues appeared positive for one of the 2 markers. Methylated ctDNA (MetctDNA) was detected in 80% of metastatic CRC and 45% of localized CRC. For samples with detectable mutations in ctDNA, MetctDNA and mutant ctDNA (MutctDNA) fractions were correlated. During follow-up of different stage CRC patients, MetctDNA changes allowed monitoring of tumor evolution. CONCLUSIONS These results indicate that MetctDNA could be used as a universal surrogate marker for tumor follow-up in CRC patients, and monitoring MetctDNA by droplet-based dPCR could avoid the need for monitoring mutations.

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LG-07 * MOSAIC GENETIC PROGRESSION MODELS OF LOW GRADE PEDIATRIC BRAIN TUMORS REVEAL UNIQUE FEATURES OF TUMOR EVOLUTION

Neuro-Oncology ◽

10.1093/neuonc/nov061.76 ◽

2015 ◽

Vol 17 (suppl 3) ◽

pp. iii19-iii19

Author(s):

C. D. Antonuk ◽

R. Levy ◽

J. Molina ◽

M. Danielpour ◽

A. Akhtar ◽

...

Keyword(s):

Brain Tumors ◽

Pediatric Brain Tumors ◽

Tumor Evolution ◽

Low Grade ◽

Pediatric Brain

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The Role of Liquid Biopsies in Pediatric Brain Tumors

Journal of Neuropathology & Experimental Neurology ◽

10.1093/jnen/nlaa068 ◽

2020 ◽

Vol 79 (9) ◽

pp. 934-940

Author(s):

Karen Tang ◽

Sharon Gardner ◽

Matija Snuderl

Keyword(s):

Brain Tumors ◽

Treatment Resistance ◽

Pediatric Brain Tumors ◽

Circulating Tumor Dna ◽

Therapeutic Monitoring ◽

Liquid Biopsies ◽

Neuropathological Diagnosis ◽

Reliable Monitoring ◽

Circulating Rna ◽

Pediatric Brain

Abstract Early detection and serial therapeutic monitoring for pediatric brain tumors are essential for diagnosis and therapeutic intervention. Currently, neuropathological diagnosis relies on biopsy of tumor tissue and surgical intervention. There is a great clinical need for less invasive methods to molecularly characterize the tumor and allow for more reliable monitoring of patients during treatment and to identify patients that might potentially benefit from targeted therapies, particularly in the setting where diagnostic tissue cannot be safely obtained. In this literature review, we highlight recent studies that describe the use of circulating tumor DNA, circulating tumor cells, circulating RNA and microRNA, and extracellular vesicles as strategies to develop liquid biopsies in pediatric central nervous system tumors. Liquid biomarkers have been demonstrated using plasma, urine, and cerebrospinal fluid. The use of liquid biopsies to help guide diagnosis, determine treatment response, and analyze mechanisms of treatment resistance is foreseeable in the future. Continued efforts to improve signal detection and standardize liquid biopsy procedures are needed for clinical application.

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