Methods
Following Institutional Review Board approval, the pathology and clinical database was queried for cases of myxopapillary ependymoma (MPE) occurring in patients less than 18 years of age diagnosed or treated at our institution between 1996 and 2018. The electronic medical record was reviewed for pertinent clinical data. The slides for available cases were reviewed, and histologic information was collected from the microscopic descriptions of the internally generated slide reviews of the other cases. Histologically, each case was evaluated for overall cellularity, mitotic activity, necrosis, microvascular proliferation, presence of an identifiable capsule, leptomeningeal involvement, and nerve root involvement. Immunohistochemical studies for H3K27me3 (C36B11 clone; Cell Signaling) and chromosomal microarray analysis were performed on all cases with available tissue (5 of 8 cases).
The OncoScan® FFPE Assay Kit (Thermo Fisher Scientific; Santa Clara, CA) was applied to isolated DNA. The technicalities of the molecular inversion probe (MIP) assay have been previously described.18 The genome-wide functional resolution of this array is approximately 500 kilobases for non-mosaic deletions and non-mosaic duplications. Deletions larger than 1 megabase, duplications larger than 2 megabases, and copy neutral loss of heterozygosity (cnLOH) larger than 10 megabases are generally reported. As a caveat, the functional resolution of this array varies significantly dependent upon size of the abnormality, probe density in region, percentage of abnormal cells, and quality of the DNA obtained, and mosaic clonal abnormalities, especially those that are represented in a minor fraction of the sample, may not be detected. . All data were analyzed and reported using the February 2009 NCBI human genome build 37.1 (hg19). The genome coordinates described are best estimates and may not represent precise breakpoints, especially for abnormalities detected in a low percentage of cells.