Identification of MYCN Copy Number Heterogeneity by Direct FISH Analysis of Neuroblastoma Preparations

Background: Amplification of MYCN and deletion of 1p in neuroblastoma are associated wtih a poor prognosis. MYCN copy numbers of 10 or greater are considered to be indicative of poor outcome. However, most molecular genetic methods for estimating the number of MYCN genes do not directly address copy number heterogeneity at the cellular level. Methods and Results: MYCN copy number was assessed by fluorescence in situ hybridization (FISH), differential polymerase chain reaction (PCR), and Southern blot analysis, using 29 patient tumors. Copy number estimates by PCR or Southern blot analyses identified MYCN amplification in 11 tumors. There was complete concordance between FISH MYCN results in all 11 tumors with amplification. FISH identified 5 tumors with marked heterogeneity for MYCN copy number. Two tumors in which a small percentage of cells within the specimen were amplified would have gone undetected by molecular genetic methods alone. Conclusions: FISH offers the advantage over the other methods of detecting heterogeneity, thereby revealing tumors with small numbers of amplified cells that would otherwise be missed and, in cases of low (3-10) copies of MYCN, distinguishing small numbers of amplified cells (poor prognosis) from triploid tumors (good prognosis). FISH also allows detection of 1p deletion using the same preparations, which represents another advantage. A combination of FISH and conventional molecular methods provides an accurate definition of sample heterogeneity, and should be routinely applied to all neuroblastomas with low levels of MYCN copy number.