Copy number alteration analysis for neuroblastoma using droplet digital polymerase chain reaction.

ABSTRACT

BACKGROUND: Neuroblastoma (NB) is a malignant tumor derived from the neural crest. MYCN amplification is a well-known adverse molecular prognostic factor for NB. Genome copy number alterations (CNAs) such as chromosome (Chr) 11q deletion, 1p deletion, and 17q gain are associated with a poor prognosis. Fluorescence in situ hybridization (FISH) and Southern blotting analysis are frequently used to detect MYCN amplification. Although comparative genomic hybridization (CGH) and single-nucleotide polymorphism (SNP) chip arrays can easily detect CNAs, these methods are impractical for clinical use due to their cost and run time. Consequently, genome copy number analysis using digital droplet PCR has become widely used to monitor CNAs. METHODS: In this study, we used digital droplet polymerase chain reaction to detect MYCN amplification and Chr 11q CNA, which was used for risk stratification according to the International Neuroblastoma Risk Group classification system. We compared the results with data from SNP chip arrays in seven NB cell lines and eight primary NB samples. RESULTS: Digital droplet PCR assays successfully detected MYCN amplification and 11q CNA. The results were very consistent with those obtained by SNP chip assay. CONCLUSIONS: Digital droplet PCR can be conducted more rapidly than FISH or Southern blotting. Accordingly, it should be useful for on-site clinical applications aimed at detecting CNAs in NB and performing risk stratification promptly after diagnosis.