supplementarymaterialsandmethodssection.docVIP

Supplementary Materials and Methods Section. Tumor samples Ninety seven fresh frozen tumor samples (20 MPNSTs, 37 neurofibromas, 27 schwannomas and 13 synovial sarcomas (SS)) were obtained from multiple institutions and included in the study. The institutional review boards have approved this study. Due to similarities in morphologic and immunohistochemical features between MPNSTs and synovial sarcoma, the definitive diagnosis of MPNST can pose a significant challenge. To ensure the application of uniform diagnostic criteria [1,47], we carried out a centralized review of all MPNST and SS cases included in the study using HE and immunohistochemical staining (reviewed by CDMF). As a molecular confirmation of the histologic diagnosis, we performed RT-PCR or fluorescence in situ hybridization (FISH) to detect the t(X;18) that defines synovial sarcoma on all MPNST and SS cases. Only cases with histological and molecular features characteristic of MPNST and SS were included. Patients with sporadic tumors and those with neurofibromatosis were represented in these tumor samples. The benign peripheral nerve sheath tumors were reviewed (RBW, PCH and SMD) and showed typical histological features. Clinicopathologic features of the tumor samples are shown in Table 1 and supplementary table 1. Gene expression profiling and analysis The Stanford cDNA microarrays used in the study contain approximately 42,000 spots representing about 28,000 genes or expressed sequence tags (/). Total RNA extraction, RNA labeling, microarray hybridization and washing of arrays and scanning were performed as previously described [48]. Only spots with a signal to background ratio of at least 2 in either the Cy3 or Cy5 channel were included. A final filtering was performed to include only genes for which 80% of the samples had good data and for which expression levels differed by at least four-fold in at least three samples analyzed. Using these criteria, 5229 genes passed the filtering and were