Quantitative assessment of copy number alterations by liquid biopsy for neuroblastoma

Abstract

Liquid biopsy, a method of detecting genomic alterations using blood specimens, has recently attracted attention as a noninvasive alternative to surgical tissue biopsy. We attempted quantitative analysis to detect amplification of MYCN (MYCNamp) and loss of heterozygosity at 11q (11qLOH), which are clinical requisites as prognostic factors of neuroblastoma (NB). In this study, cell‐free DNA (cfDNA) was extracted from plasma samples from 24 NB patients at diagnosis. Copy numbers of MYCN and NAGK genes were quantitatively analyzed by droplet digital PCR (ddPCR). 11qLOH was also assessed by detecting allelic imbalances of heterozygous single nucleotide polymorphisms in the 11q region. The results obtained were compared to those of specimens from tumor tissues. The correlation coefficient of MYCN copy number of cfDNA and tumor DNA was 0.88 (p < 0.00001). 11qLOH was also accurately detected from cfDNA, except for one case with localized NB. Given the high accuracy of liquid biopsy, to investigate components of cfDNA, the proportion of tumor‐derived DNA was estimated by examining the variant allele frequency of tumor‐specific mutations in cfDNA. The proportion of tumor‐derived DNA in cfDNA was 42.5% (range, 16.9%–55.9%), suggesting sufficient sensitivity of liquid biopsy for NB. In conclusion, MYCN copy number and 11qLOH could be quantitatively analyzed in plasma cfDNA by ddPCR assay. These results suggest that plasma cfDNA can be substituted for tumor DNA and can also be applied for comprehensive genomic profiling analysis.

Clinical Diagnostic Performance of Droplet Digital PCR for Suspected Bloodstream Infections

“…Therefore, external references with variations in PCR efficiency are not necessary anymore ( 11 ). It has been used in a lot of clinical fields, such as liquid biopsies for cancer monitoring and noninvasive prenatal testing for genetic abnormality detection ( 12 – 14 ). Recently, ddPCR has shown promising potential in resolving polymicrobial infection since it simultaneously achieves unprecedented high sensitivity (able to detect pathogens at low concentrations of as few as 10 CFU/mL) in an about 4-h turnaround time ( 15 ).…”

Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study

“…At present, new nucleic acid detection techniques have been used to detect pathogenic microorganisms. Droplet digital PCR (ddPCR) is a method of absolute nucleic acid quantification by using Poisson statistical analysis of the number of positive and negative droplets and has been proven to achieve higher accuracy and sensitivity than qPCR ( Shirai et al., 2022 ). It has been used in a lot of clinical fields, such as liquid biopsies for cancer monitoring and noninvasive prenatal testing for genetic abnormality detection( Cainap et al., 2021 ; Boldrin et al., 2022 ).…”

Late effects and treatment related morbidity associated with treatment of neuroblastoma patients in a tertiary paediatric centre

“…29 Additionally, liquid biopsy studies have demonstrated that cellfree DNA (cfDNA) is a sensitive method of detecting minimal residual disease (MRD) in adult cancers and has been used for risk stratification in adult clinical trials. 30 Liquid biopsy could likewise be applied in neuroblastoma patients, 31 where cfDNA could be used to guide intensification or de-intensification of treatment as children progress through therapy, with the aim to reduce the burden of late effects if a good MRD response is obtained. It is important to emphasize that current risk stratification and treatment strategies need to be improved to reduce the significant burden of late effects to allow for improved patient management, with the hope that modern MRD techniques and molecularly targeted agents will inform future customized therapies.…”