INTRODUCTION

Ancillary studies including immunohistochemistry, molecular diagnostics, and cytogenetics play important roles in the diagnosis, subtyping, and prognostication of hematopoietic, epithelial, and mesenchymal neoplasms. The advent of clinically useful techniques for the detection of mutations, translocations, and copy number alterations has greatly expanded the utility of molecular diagnostics in the work-up of malignant neoplasms. Ancillary studies appear to be particularly helpful in the investigation of musculoskeletal lesions including lymphomas. Chromosomal translocations and mutations appear to be of greater diagnostic aid in bone and soft tissue lesions than in neoplasms of epithelial tissues. A subset of sarcomas bears chromosomal anomalies including reciprocal translocations, deletions, mutations, and amplifications which appear to be specific for certain histopathologic types. Mutations such as those occurring in the KIT and platelet derived growth factor alpha genes are important for the diagnosis of gastrointestinal stromal tumors as well as the prediction of response to directed therapy (Gleevec). Similarly, the SYT-SSX fusion transcript resulting from the t(X;18)(p11;q11) appears to be specific for synovial sarcoma. Of equal interest, both diagnostically and pathogenetically, are the translocations and fusion genes involving the EWS gene (22q12) which appear to define a Ewing family of sarcomas comprising the entities intra-abdominal desmoplastic small round tumor, myxoid chondrosarcoma, Ewing sarcoma, and primitive neuroectodermal tumor. These findings have facilitated the development of a molecular approach to soft tissue sarcomas. On this basis, soft tissue sarcomas currently can be divided into two groups. One group has specific chromosomal abnormalities (gene mutations and translocations) while the other shows complex often non-specific karyotypic abnormalities.