Increased plasma concentration of cell-free DNA precedes disease recurrence in children with high-risk neuroblastoma

Abstract Background: Neuroblastoma is the most common extracranial solid tumor of childhood. The high rate of recurrence is associated with a low survival rate for patients with high-risk neuroblastoma. There is thus an urgent need to identify effective predictive biomarkers of disease recurrence. Methods: A total of 116 patients with high-risk neuroblastoma were recruited at Beijing Children’s Hospital between February 2015 and December 2017. All patients received multidisciplinary treatment, were evaluated for the therapeutic response, and then initiated on maintenance treatment. Blood samples were collected at the beginning of maintenance treatment, every 3 months thereafter, and at the time of disease recurrence. Plasma levels of cell-free DNA (cfDNA) were quantified by qPCR. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the ability of plasma cfDNA concentration to predict recurrence. Results: Of the 116 patients, 36 (31.0%) developed recurrence during maintenance treatment. The median time to recurrence was 19.00, 9.00, and 8.00 months for patients who had achieved complete response (n = 6), partial response (n = 25), and stable disease (n = 5), respectively, after multidisciplinary treatment. The median plasma cfDNA concentration at the time of recurrence was significantly higher than the concentration in recurrence-free patients throughout maintenance treatment (29.34 ng/mL vs 10.32 ng/mL). Patients recorded a plasma cfDNA level ≥29 ng/mL an average of 0.55 months before diagnosis of disease recurrence. ROC analysis of the power of plasma cfDNA to distinguish between patients with or without recurrence yielded an area under the curve of 0.825, with optimal sensitivity and specificity of 80.6% and 71.3%, respectively, at a cfDNA level of 12.93 ng/mL. Conclusions: High plasma cfDNA concentration is a potential molecular marker to signal disease recurrence in patients with high-risk neuroblastoma.

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Increased plasma concentration of cell-free DNA precedes disease recurrence in children with high-risk neuroblastoma

10.21203/rs.2.13924/v4 ◽

2020 ◽

Author(s):

Yan Su ◽

Lijun Wang ◽

Chiyi Jiang ◽

Zhixia Yue ◽

Hongjun Fan ◽

...

Keyword(s):

High Risk ◽

Maintenance Treatment ◽

Multidisciplinary Treatment ◽

Area Under The Curve ◽

Predictive Biomarkers ◽

Disease Recurrence ◽

High Rate ◽

Roc Curve Analysis ◽

Cell Free Dna ◽

Free Dna

Abstract Background: Neuroblastoma is the most common extracranial solid tumor of childhood. The high rate of recurrence is associated with a low survival rate for patients with high-risk neuroblastoma. There is thus an urgent need to identify effective predictive biomarkers of disease recurrence. Methods: A total of 116 patients with high-risk neuroblastoma were recruited at Beijing Children’s Hospital between February 2015 and December 2017. All patients received multidisciplinary treatment, were evaluated for the therapeutic response, and then initiated on maintenance treatment. Blood samples were collected at the beginning of maintenance treatment, every 3 months thereafter, and at the time of disease recurrence. Plasma levels of cell-free DNA (cfDNA) were quantified by qPCR. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the ability of plasma cfDNA concentration to predict recurrence. Results: Of the 116 patients, 36 (31.0%) developed recurrence during maintenance treatment. The median time to recurrence was 19.00, 9.00, and 8.00 months for patients who had achieved complete response (n = 6), partial response (n = 25), and stable disease (n = 5), respectively, after multidisciplinary treatment. The median plasma cfDNA concentration at the time of recurrence was significantly higher than the concentration in recurrence-free patients throughout maintenance treatment (29.34 ng/mL vs 10.32 ng/mL). Patients recorded a plasma cfDNA level ≥29 ng/mL an average of 0.55 months before diagnosis of disease recurrence. ROC analysis of the power of plasma cfDNA to distinguish between patients with or without recurrence yielded an area under the curve of 0.825, with optimal sensitivity and specificity of 80.6% and 71.3%, respectively, at a cfDNA level of 12.93 ng/mL. Conclusions: High plasma cfDNA concentration is a potential molecular marker to signal disease recurrence in patients with high-risk neuroblastoma.

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High concentration of plasma cell free DNA alerting disease recurrence in high risk neuroblastoma children

10.21203/rs.2.13924/v1 ◽

2019 ◽

Author(s):

Yan Su ◽

Lijun Wang ◽

Chiyi Jiang ◽

Zhixia Yue ◽

Hongjun Fan ◽

...

Keyword(s):

High Risk ◽

Plasma Cell ◽

Maintenance Treatment ◽

Treatment Phase ◽

Disease Recurrence ◽

High Rate ◽

High Concentration ◽

Cell Free Dna ◽

Free Dna ◽

High Level

Abstract Background Neuroblastoma is the third-most common cancer in children. The high rate of tumor recurrence accounts for a low survival rate in high risk neuroblastoma. Therefore it is clinically of extreme importance to find an effective biomarker for alerting disease recurrence.Methods Total 116 high risk neuroblastoma patients were recruited in Beijing Children’s Hospital from February, 2015 to December, 2017. All patients had received multiple-disciplinary treatment, then went into maintenance treatment phase after evaluation. Blood samples were collected to quantify plasma cell-free DNA (cfDNA) at time points of the beginning of maintenance treatment, every three months afterwards, and diagnosis of recurrence.Results Results showed that 36 high risk neuroblastoma patients developed recurrence during maintenance treatment. The plasma cfDNA concentration was significantly higher in recurrence than in event-free patients (29.34 ng/ml VS 10.32 ng/ml). The time span of cfDNA level higher than 29 ng/ml was consistently detected ahead of recurrence at mean of 0.55 months. The ROC analysis showed that AUC was 0.825, optimal sensitivity and specificity of 80.6% and 71.3% respectively, at cfDNA level of 12.93 ng/ml.Conclusions We concluded that high level of plasma cfDNA could serve as a promising molecular marker to alert recurrence disease in high risk neuroblastoma children.

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Increased plasma concentration of cell-free DNA precedes disease recurrence in children with high-risk neuroblastoma

10.21203/rs.2.13924/v2 ◽

2020 ◽

Author(s):

Yan Su ◽

Lijun Wang ◽

Chiyi Jiang ◽

Zhixia Yue ◽

Hongjun Fan ◽

...

Keyword(s):

High Risk ◽

Maintenance Treatment ◽

Roc Analysis ◽

Treatment Phase ◽

Disease Recurrence ◽

High Rate ◽

Cell Free Dna ◽

Free Dna ◽

High Level ◽

Cancer In Children

Abstract Background Neuroblastoma is the third-most common cancer in children. The high rate of tumor recurrence accounts for a low survival rate in high risk neuroblastoma. Therefore it is clinically of extreme importance to find an effective biomarker for alerting disease recurrence.Methods Total 116 high risk neuroblastoma patients were recruited in Beijing Children's Hospital from February, 2015 to December, 2017. All patients had received multiple-disciplinary treatment, then went into maintenance treatment phase after evaluation. Blood samples were collected to quantify plasma cell-free DNA (cfDNA) at time points of the beginning of maintenance treatment, every three months afterwards, and diagnosis of recurrence.Results Results showed that 36 high risk neuroblastoma patients developed recurrence during maintenance treatment. The plasma cfDNA concentration was significantly higher in recurrence than in event-free patients (29.34 ng/ml VS 10.32 ng/ml). The time span of cfDNA level higher than 29 ng/ml was consistently detected ahead of recurrence at mean of 0.55 months. The ROC analysis showed that AUC was 0.825, optimal sensitivity and specificity of 80.6% and 71.3% respectively, at cfDNA level of 12.93 ng/ml.Conclusions We concluded that high level of plasma cfDNA could serve as a promising molecular marker to alert recurrence disease in high risk neuroblastoma children.

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Implementation of cell-free DNA-based non-invasive prenatal testing in a National Health Service Regional Genetics Laboratory

Genetics Research ◽

10.1017/s0016672319000119 ◽

2019 ◽

Vol 101 ◽

Cited By ~ 1

Author(s):

Fiona S. Togneri ◽

Mark D. Kilby ◽

Elizabeth Young ◽

Samantha Court ◽

Denise Williams ◽

...

Keyword(s):

National Health Service ◽

High Risk ◽

Health Service ◽

National Health ◽

Prenatal Testing ◽

Low Risk ◽

Trisomy 13 ◽

Cell Free Dna ◽

Non Invasive ◽

Free Dna

Abstract Background Non-invasive prenatal testing (NIPT) for the detection of foetal aneuploidy through analysis of cell-free DNA (cfDNA) in maternal blood is offered routinely by many healthcare providers across the developed world. This testing has recently been recommended for evaluative implementation in the UK National Health Service (NHS) foetal anomaly screening pathway as a contingent screen following an increased risk of trisomy 21, 18 or 13. In preparation for delivering a national service, we have implemented cfDNA-based NIPT in our Regional Genetics Laboratory. Here, we describe our validation and verification processes and initial experiences of the technology prior to rollout of a national screening service. Methods Data are presented from more than 1000 patients (215 retrospective and 840 prospective) from ‘high- and low-risk pregnancies’ with outcome data following birth or confirmatory invasive prenatal sampling. NIPT was by the Illumina Verifi® test. Results Our data confirm a high-fidelity service with a failure rate of ~0.24% and a high sensitivity and specificity for the detection of foetal trisomy 13, 18 and 21. Secondly, the data show that a significant proportion of patients continue their pregnancies without prenatal invasive testing or intervention after receiving a high-risk cfDNA-based result. A total of 46.5% of patients referred to date were referred for reasons other than high screen risk. Ten percent (76/840 clinical service referrals) of patients were referred with ultrasonographic finding of a foetal structural anomaly, and data analysis indicates high- and low-risk scan indications for NIPT. Conclusions NIPT can be successfully implemented into NHS regional genetics laboratories to provide high-quality services. NHS provision of NIPT in patients with high-risk screen results will allow for a reduction of invasive testing and partially improve equality of access to cfDNA-based NIPT in the pregnant population. Patients at low risk for a classic trisomy or with other clinical indications are likely to continue to access cfDNA-based NIPT as a private test.

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Abstract 2592: Whole-exome sequencing cell free DNA analysis documents new tumor specific alterations at relapse of high-risk pediatric cancers

10.1158/1538-7445.am2018-2592 ◽

2018 ◽

Author(s):

Mathieu Chicard ◽

Adrien Danzon ◽

Nathalie Clémént ◽

Irene Jimenez ◽

Eve Lapouble ◽

...

Keyword(s):

High Risk ◽

Exome Sequencing ◽

Whole Exome Sequencing ◽

Dna Analysis ◽

Cell Free Dna ◽

Pediatric Cancers ◽

Free Dna ◽

Whole Exome

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Cell-free DNA testing in the maternal blood in high-risk pregnancies after first-trimester combined screening

Prenatal Diagnosis ◽

10.1002/pd.4773 ◽

2016 ◽

Vol 36 (3) ◽

pp. 232-236 ◽

Cited By ~ 8

Author(s):

Nicola Persico ◽

Simona Boito ◽

Benedetta Ischia ◽

Adalgisa Cordisco ◽

Valentina De Robertis ◽

...

Keyword(s):

High Risk ◽

First Trimester ◽

Maternal Blood ◽

Dna Testing ◽

Cell Free Dna ◽

Free Dna

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Cell-Free DNA Testing: What Is the Reason Why High-Risk Women Choose It?

Fetal Diagnosis and Therapy ◽

10.1159/000509796 ◽

2020 ◽

pp. 1-6

Author(s):

Leticia Benítez-Quintanilla ◽

Montse Pauta ◽

Isabel Matas ◽

Irene Madrigal ◽

Antoni Borrell

Keyword(s):

High Risk ◽

Dna Testing ◽

Cell Free Dna ◽

High Risk Women ◽

Free Dna

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5-hydroxymethylcytosine as a liquid biopsy biomarker in mCRPC.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.6_suppl.148 ◽

2021 ◽

Vol 39 (6_suppl) ◽

pp. 148-148

Author(s):

Martin Sjöström ◽

Shuang Zhao ◽

Eric Jay Small ◽

Yuhong Ning ◽

Corinne Maurice-Dror ◽

...

Keyword(s):

Gene Expression ◽

Prostate Cancer ◽

Overall Survival ◽

High Risk ◽

Liquid Biopsy ◽

Copy Number ◽

Whole Genome ◽

Cell Free Dna ◽

Free Dna ◽

Disease Specific

148 Background: 5-hydroxymethylcytosine (5hmC) is an epigenetic modification which regulates gene expression and is associated with active transcription. The optimization of 5hmC sequencing in cell-free DNA (cfDNA) could therefore enable assessment of gene activity through a liquid biopsy. We aimed to investigate the 5hmC landscape of metastatic castration-resistant prostate cancer (mCRPC) and to evaluate the potential of 5hmC modifications in cfDNA as biomarkers of outcome in mCRPC patients. Methods: Genome-wide 5hmC modifications were analyzed with a low-input whole-genome 5hmC sequencing method based on selective chemical labeling in DNA from 93 mCRPC tissue biopsies previously profiled with whole-genome sequencing (WGS), RNA-sequencing and whole-genome bisulfite sequencing (WGBS). In addition, we analyzed 64 cell-free DNA (cfDNA) samples, from men with mCRPC before first-line abiraterone or enzalutamide, with both 5hmC sequencing and a conventional targeted ctDNA panel assessing common genomic alterations. Results: In mCRPC tissue samples, 5hmC enrichment was more strongly associated with gene expression than promoter methylation or copy number. Among cancer hallmark pathways, the androgen response genes had the strongest association between 5hmC and gene expression, suggesting a disease specific marking of gene activation. 5hmC patterns in cfDNA could be used to estimate the circulating tumor DNA fraction (ct-fraction), which was prognostic for overall survival (tertiles of ct-fraction, HR = 1.6 95%CI 1.1-2.3, p = 0.007). Further, 5hmC levels were indicative of gain of oncogene activity (such as AR, MYC, and PIK3CA) and loss of tumor suppressor gene activity (such as RB1, TP53 and BRCA2). The number of alterations, by 5hmC levels, of common drivers of mCRPC was prognostic for overall survival, also after adjusting for ct-fraction (adjusted p = 0.00001), and the prognostic value of common alterations detected by 5hmC sequencing versus conventional targeted ctDNA sequencing was similar. Finally, 5hmC levels in cfDNA of genes not significantly altered by copy number gain or loss (and thus not routinely included in targeted ctDNA sequencing assays), such as TOP2A and EZH2, identified a high-risk subgroup of mCRPC, which was highly prognostic for overall survival independent of ct-fraction (adjusted HR = 1.8 95%CI 1.2-2.8, p = 0.007). Conclusions: 5hmC in mCRPC tissue demonstrated an association with gene expression that was highest for prostate cancer driver genes, highlighting the ability to track disease-specific biology. 5hmC in cfDNA from men with mCRPC can be used to estimate the ct-fraction of the sample, infer activity gain and loss of common drivers of mCRPC, and identify high-risk groups of mCRPC based on alterations not commonly detected with conventional ctDNA sequencing, showing its potential as a liquid biomarker. Further studies are aimed at optimizing and validating 5hmC-based biomarkers in larger cohorts.

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