Background: Copy number aberrations (CNA) in Neuroblastoma contribute to prognosis and treatment stratification. Single nucleotide polymorphism (SNP) arrays can identify all clinically important CNAs in Neuroblastoma with the exception of balanced translocations, and can detect important rare genomic abnormalities. We compared SNP arrays from 99 neuroblastoma samples and 13 neuroblastoma cell lines with matching karyotypes and clinical data where available. Our goals were to characterise the typical array features of Neuroblastoma, including MYCN amplification, 11q deletion and other segmental CNAs, and define the clinical utility of molecular karyotyping.
Results: Classical karyotyping had a poor diagnostic yield, including false negative results (48%). In all instances, significant CNAs were detected in these same samples by SNP array. The typical features of MYCN amplification on the array platform were alleleic imbalance and saturation of the smoothed logR values. We defined the relationship between absolute copy numbers of MYCN and these array features using orthogonal data, including a digital droplet PCR (ddPCR) assay we developed. No case with true MYCN amplification was missed by array. In serial dilutions of MYCN amplified cell line DNA, ddPCR MYCN assay was an extremely sensitive means to detect MYCN amplification.
Features usually undetected by karyotyping, segmental deletions or copy number gains, are frequently observed in arrays, and the number of segmental anomalies detected by SNP array was a strong predictor of poor outcome (p = 0.000007, n= 42). The minimal overlapping 11q deletion region of our cohort matches those previously reported. Interestingly, several rare but likely pathogenic amplification events at loci other than MYCN were identified.
Conclusion: SNP arrays significantly improve the accuracy of genomic risk assessment in Neuroblastoma and expand the range of CNAs detected. They obviate the need for conventional karyotype. There are novel, recurrent gene amplifications that may be important driver events in Neuroblastoma.