The patient was a 4 year old male diagnosed with hepatoblastoma. DNA was extracted
from paraffin embedded tumor sections and analyzed using the OncoScan CNV assay. Tissue
from the same block was independently analyzed on the a targeted DNA hybrid capture
NGS platform. Initial microarray results indicated a copy number gain at 1q32.1 (PIK3C2B,
MDM4), copy number gains on Chromosome 20 and multiple regions of loss of heterozygosity.
In contrast, data from the NGS assay indicated whole chromosome gains of 2, 5, 10
and 17 along with the copy number gain at 1q32.1 (PIK3C2B, MDM4). In order to better
understand the difference between the two platforms, the slide was examined histologically.
Four distinct morphologies were present on the slide: fetal epithelial hepatoblastoma,
embryonal epithelial hepatoblastoma, mesenchymal hepatoblastoma and normal liver tissue.
Tissue was microdissected to extract DNA and run a microarray for each of the four
areas. DNA extracted from mesenchymal hepatoblastoma tissue resulted in an array with
a high level of background noise. The fetal tissue region exhibited copy number gains
in chromosome 2, 5, 8, 12, 17, 19 and 20. The embryonal tissue exhibited copy number
gains in 2, 5, 8, 17 and 20 along with the 1q32.1 (PIK3C2B, MDM4) region. This analysis
shows different genomic clones within the same area of hepatoblastoma. From a technical
standpoint, these results demonstrate that multiple clones may mask the copy number
analysis of a heterogeneous tumor.
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