Genome wide aneuploidy scores and detection of sub-chromosomal copy number changes in PDGFA, TERT, TBX1, EGFR, BRAF, EXT1, CDKN2A/B, PTEN, EXT2, EED, IDH2, TP53, NF1, and SUZ12 allow for detection of 50% of MPNST at 97% specificity. Here, SUZ12 is linked to malignant peripheral nerve sheath tumor.