Validating MYCN Copy Number Estimation

For validation of WES-based estimation of MYCN copy numbers, a SNP array (Cytoscan HD, ThermoFisher Scientific, #901835) was performed for selected patient samples as in ref. ^{15 (link)}. CEL files with intensity probe signals were analysed using the Chromosome Analysis Suite (ChAS) software version 4.1.0.90 (r29400) and converted to CYCHP files. Copy numbers are visualised using the allele difference plot, weighted log2 ratio and the smoothed signal. The smoothed signal is used to directly estimate copy numbers.
MYCN copy number was detected on FFPE tissue on single-cell level using FISH analysis. The hybridisation probe XL MYCN amp (MetaSystems) consists of a green-labelled probe hybridising to the MYCN gene region at 2p24 and an orange-labelled probe hybridising to the NMI gene region at 2q23 as reference. Data interpretation was done according to INRG Biology guidelines^{69 (link)}.