Detection of circulating tumor-derived material (cTM) in the peripheral blood (PB) of cancer patients has been shown to be useful in early diagnosis, prediction of prognosis, and disease monitoring. However, it has not yet been thoroughly evaluated for pediatric sarcoma patients.We searched the PubMed and EMBASE databases for studies reporting the detection of circulating tumor cells, circulating tumor DNA, and circulating RNA in PB of pediatric sarcoma patients. Data on performance in identifying cTM and its applicability in diagnosis, and evaluation of tumor characteristics, prognostic factors, and treatment response was extracted from publications.A total of 79 studies were assigned for the present systematic review, including detection of circulating tumor cells (116 patients), circulating tumor DNA (716 patients), and circulating RNA (2887 patients). Circulating tumor cells were detected in 76% of patients. Circulating DNA was detected in 63% by targeted NGS, 66% by shallow WGS, and 79% by digital droplet PCR. Circulating RNA was detected in 37% of patients.Of the cTM from Ewing's sarcoma and rhabdomyosarcoma ctDNA proved to be the best target for clinical application including diagnosis, tumor characterization, prognosis, and monitoring of disease progression and treatment response. For osteosarcoma the most promising targets are copy number alterations or patient specific micro RNAs, however, further investigations are needed to obtain consensus on clinical utility.
Background: Genomic profiling in advanced Non-Small Cell Lung cancer (NSCLC) can reveal Actionable Molecular Alterations (AMAs). Our study aims to investigate clinical relevance of re-biopsy after first line treatment, by reporting on acquired and persistent AMAs and potential targeted treatments in a real-time cohort of NSCLC patients. Methods: Patients with advanced NSCLC receiving first-line treatment were prospectively included in an observational study (NCT03512847). Genomic profiling was performed by TruSight Oncology 500 HT gene panel on tumor tissue collected at diagnosis and at time of progression. Results: The 92 patients re-biopsied at progression had received immunotherapy (n = 44), chemotherapy (n = 44), or combination treatment (n = 4). In 87 of these patients (95%), successful genomic profiling was performed at both the diagnostic biopsy and the re-biopsy. In 74 patients (85%), ≥1 AMA were found. The AMAs were acquired in 28%. The most frequent AMAs were observed in TP53 (45%), KRAS (24%), PIK3CA (6%), and FGFR1 (6%). Only five patients (5%) received targeted treatment mainly due to deterioration in performance status. Conclusions: Re-biopsy at progression revealed acquired AMAs in approximately one third of patients, and 85% had at least one AMA with the potential of receiving targeted treatment, thus strengthening the clinical relevance of re-biopsy.
Abstract Ependymoma is the second most common malignant brain tumor in children. The etiology is largely unknown and germline DNA sequencing studies focusing on childhood ependymoma are limited. We therefore performed germline whole-genome sequencing on a population-based cohort of children diagnosed with ependymoma in Denmark over the past 20 years (n = 43). Single nucleotide and structural germline variants in 457 cancer related genes and 2986 highly evolutionarily constrained genes were assessed in 37 children with normal tissue available for sequencing. Molecular ependymoma classification was performed using DNA methylation profiling for 39 children with available tumor tissue. Pathogenic germline variants in known cancer predisposition genes were detected in 11% (4/37; NF2 , LZTR1 , NF1 & TP53 ). However, DNA methylation profiling resulted in revision of the histopathological ependymoma diagnosis to non-ependymoma tumor types in 8% (3/39). This included the two children with pathogenic germline variants in TP53 and NF1 whose tumors were reclassified to a diffuse midline glioma and a rosette-forming glioneuronal tumor, respectively. Consequently, 50% (2/4) of children with pathogenic germline variants in fact had other tumor types. A meta-analysis combining our findings with pediatric pan-cancer germline sequencing studies showed an overall frequency of pathogenic germline variants of 3.4% (7/207) in children with ependymoma. In summary, less than 4% of childhood ependymoma is explained by genetic predisposition, virtually restricted to pathogenic variants in NF2 and NF1 . For children with other cancer predisposition syndromes, diagnostic reconsideration is recommended for ependymomas without molecular classification. Additionally, LZTR1 is suggested as a novel putative ependymoma predisposition gene.
Selecting patients for early clinical trials is a challenging process and clinicians lack sufficient tools to predict overall survival (OS). Circulating cell-free DNA (cfDNA) has recently been shown to be a promising prognostic biomarker. The aim of this study was to investigate whether baseline cfDNA measurement could improve the prognostic information of the Royal Marsden Hospital (RMH) score. Solid tumour patients referred for phase I trials were included in the Copenhagen Personalized Oncology (CoPPO) programme. Baseline characteristics were collected prospectively, including the RMH prognostic score, Eastern Cooperative Oncology Group (ECOG) performance status and concentration of cfDNA per millilitre plasma. Cox proportional hazards model was used to assess the prognostic value of baseline variables. Plasma cfDNA concentration was quantifiable in 302 patients out of a total of 419 included in the study period of 2 years and 5 months. The RMH score was confirmed to be associated with OS. Cell-free DNA was shown to be an independent prognostic marker of OS and improved the risk model, including RMH, performance status and age. Furthermore, both plasma cfDNA concentration and RMH score were associated with treatment allocation (p < 0.00001). Our model based on RMH score, age, ECOG performance status and cfDNA improved prediction of OS and constitutes a clinically valuable tool when selecting patients for early clinical trials. An interactive version of the prognostic model is published on http://bit.ly/phase1survival .
Abstract Introduction: Glioblastoma (GBM) is an aggressive brain cancer with a median overall survival of 16-24 months. Evaluation of treatment effect can be difficult as pseudo progression is seen in approximately 15% of patients. Hence, effective treatment can be stopped prematurely and no approved or standard second line treatment exist. Genomic alterations during treatment can cause treatment resistance and treatment failure. In order to investigate the genomic alterations, consecutive tissue samples are wanted. However, this is often not possible due to risk doing surgery. Therefore, liquid biopsies from plasma, containing circulating cell-free DNA (cfDNA) and circulating cell-free tumor DNA (ctDNA) might be an alternative. Based on findings by our group, we aim to improve treatment evaluation and suggest targeted treatment possibilities by investigating the role of cfDNA and ctDNA in a large prospective cohort, included from a neurooncological out-patient clinic. Materials and Methods: Newly diagnosed patients with GBM, a performance status of 0-1 and planned for concurrent chemo/radiation will be eligible. Whole genome sequencing (WGS) will be done on tissue. Peripheral blood will be collected in cell stabilizing Blood Collection Tubes (STRECK) and cfDNA quantified on a Qubit Fluorometer. Samples will be collected before the concurrent treatment and at fixed time points until progression with a total of 8-10 samples per patient. For the ctDNA analyses, a patient specific tumor mutation will be selected based upon WGS from tumor tissue. The identified mutation will be quantified in plasma (ctDNA) by droplet digital PCR (ddPCR). Dual labeled fluorescent probes for the mutation and the wild type loci will be used and PCR reaction mixtures will be run. Mutant allele fractions (AFs) ≥0.001 (0.1%) will be detected. An increase in ctDNA AF will be recorded if the AF increases from non-detectable to detectable levels (AF ≥ 0.001) or increases in two consecutive samples. Results: Inclusion began in June 2022 and by time of abstract deadline, we have 27 patients included. Of these, 16 have completed the concurrent setting with a total of five samples per patient. One patient has died and two have progressed. Hence, 24 patients are still on-treatment and sampling and accrual will continue. The first analyses for cfDNA will be run in the winter of 2022/2023 and results will be presented at the conference. CtDNA analyses are planned for autumn 2023. Expected Impact: The expected impacts of this study are specifically in two clinical areas: treatment evaluation and development of new treatment strategies. We aim to 1) find correlation between cfDNA/ctDNA and the clinical course2) detect a relapse earlier than imaging with MRI and FET/PET analyses3) aid to diagnose pseudo progression4) use ctDNA for detection of clonal selection5) test concordance between mutations detected in tissue and in plasma Citation Format: Dorte Schou Nørøxe, Lise Barlebo Ahlborn, Vincent Fougner, Thomas Urup, Benedikte Hasselbalch, Christina Westmose Yde, Hans Skovgaard Poulsen, Ulrik Lassen. Tracking tumor mutations in ctDNA through repetitive plasma samples in patients with newly diagnosed brain cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1046.
Abstract Background: BRAF inhibitors have been approved in BRAF mutated malignant melanoma. However, in other BRAF mutated cancers, the effect of BRAF inhibition has been studied less extensively. BRAF mutated non-melanoma cancer patients (pts) were identified in a prospective genomic profiling study. The effect of targeted treatment was assessed by BRAF mutant allele fraction (AF) in circulating tumor DNA (ctDNA) and radiological response. Methods: Pts had tumor biopsies performed at enrolment and, if feasible, on or after treatment. Biopsies were subjected to whole exome sequencing, RNA sequencing and SNP array. Blood samples for ctDNA analysis were collected at baseline and longitudinally during treatment. Mutant BRAF fragments were quantified using droplet digital PCR (ddPCR) or by targeted next generation sequencing (NGS). Radiological response was evaluated according to RECIST 1.1. Results: Twenty-two BRAF mutated non-melanoma cancer pts (lung n=2, colorectal n=14, bile duct n=4, prostate n=1, pancreas n=1) were identified out of a total of 405 (5 %) pts enrolled in the Copenhagen Prospective Personalized Oncology (CoPPO) study. In all tumors we identified the BRAF V600E mutation except in one prostate cancer pt (BRAF K601E). Fifteen pts were treated with dabrafenib/trametinib (lung, bile duct), vemurafenib/panitumumab +/- irinotecan (colorectal) or vemurafenib (pancreas, prostate). Two pts were non-evaluable because one patient requested early termination and one has pending tumor evaluation. All pts had tumor reduction, except one patient with colon cancer. Six out of 13 (46%) pts achieved partial response (lung n=2, bile duct n=1, colorectal n= 3) and 7/13 (44%) had stable disease (prostate n=1, bile duct n=1, colorectal n= 5) as best response according to RECIST 1.1. Median progression-free survival was 20 weeks. Eighteen pts analysed by ddPCR or NGS at baseline had detectable mutant BRAF in the plasma obtained before initiation of therapy. Eight of the 18 pts had ctDNA assessed during treatment and all presented with a reduction in mutant BRAF AF corresponding to a reduction in tumor volume. Moreover, in 5/8 pts, time of best radiological response coincided with the lowest detectable BRAF mutant AF. Analysis of on- and post treatment biopsies and matched ctDNA samples are pending to identify putative mechanisms of resistance and will be reported at the meeting. Conclusion: Targeted therapy seems active in BRAF mutated non-melanoma cancer pts and treatment response is evaluable by monitoring mutant BRAF in ctDNA during therapy. Citation Format: Lise Barlebo Ahlborn, Ida Viller Tuxen, Olga Oestrup, Ane Yde Schmidt, Cecilia Brunhoff Håkansson, Finn Celius Nielsen, Ulrik Lassen, Christina Westmose Yde, Morten Mau-Sorensen. BRAF mutant allele fraction in circulating tumor DNA as marker of treatment response in BRAF mutated non malignant melanoma cancers identified in the Copenhagen Prospective Personalized Oncology study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5393. doi:10.1158/1538-7445.AM2017-5393
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