1. Multiplexed Quantification of Four Neuroblastoma DNA Targets in a Single Droplet Digital PCR Reaction
- Author
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Rasmus B. Linke, Karin Schmelz, Joern Toedling, Constantin Peitz, Angelika Eggert, Matthias Fischer, Clemens Messerschmidt, Maddalena Grimaldi, Hedwig E. Deubzer, Dieter Beule, Johannes H. Schulte, Marco Lodrini, Kathy Astrahantseff, Ulrich Keilholz, and Annika Sprüssel
- Subjects
0301 basic medicine ,DNA Copy Number Variations ,Sensitivity and Specificity ,Pathology and Forensic Medicine ,Neuroblastoma ,03 medical and health sciences ,chemistry.chemical_compound ,Exon ,0302 clinical medicine ,Cell Line, Tumor ,Reference genes ,Blood plasma ,medicine ,Humans ,Anaplastic Lymphoma Kinase ,Digital polymerase chain reaction ,Liquid biopsy ,Alleles ,N-Myc Proto-Oncogene Protein ,Liquid Biopsy ,Reproducibility of Results ,Exons ,medicine.disease ,Molecular biology ,Data Accuracy ,030104 developmental biology ,chemistry ,030220 oncology & carcinogenesis ,Mutation ,Molecular Medicine ,Primer (molecular biology) ,Cell-Free Nucleic Acids ,Multiplex Polymerase Chain Reaction ,DNA - Abstract
The detection and characterization of cell-free DNA (cfDNA) in peripheral blood from neuroblastoma patients may serve as a minimally invasive approach to liquid biopsy. Major challenges in the analysis of cfDNA purified from blood samples are small sample volumes and low cfDNA concentrations. Droplet digital PCR (ddPCR) is a technology suitable for analyzing low levels of cfDNA. Reported here are two quadruplexed ddPCR assay protocols that reliably quantify MYCN and ALK copy numbers in a single reaction together with the two reference genes, NAGK and AFF3, and accurately estimate ALKF1174L (exon 23 position 3522, C>A) and ALKR1275Q (exon 25 position 3824, G>A) mutant allele fractions using cfDNA as input. The separation of positive and negative droplets was optimized for detecting two targets in each ddPCR fluorescence channel by the adjustment of the probe and primer concentrations of each target molecule. The quadruplexed assays were validated using a panel of 10 neuroblastoma cell lines and paired blood plasma and primary neuroblastoma samples from nine patients. Accuracy and sensitivity thresholds in quadruplexed assays corresponded well with those from the respective duplexed assays. Presented are two robust quadruplexed ddPCR protocols applicable in the routine clinical setting and that require only minimal plasma volumes for the assessment of MYCN and ALK oncogene status.
- Published
- 2020